Question: error in R when installing DESeq2 package
0
gravatar for F
3.5 years ago by
F3.4k
Iran
F3.4k wrote:

sorry guys,

whenever im trying, this is the error

what does this mean please? how i can fix it?

> source("https://bioconductor.org/biocLite.R")
https:// URLs are not supported by the default method: trying "libcurl"
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
>

R software error • 6.4k views
ADD COMMENTlink modified 2.4 years ago by csclaros20 • written 3.5 years ago by F3.4k
2
gravatar for csclaros
2.4 years ago by
csclaros20
csclaros20 wrote:

Hi! You need to run this in your terminal before installing anything in Bioconductor/R: sudo apt-get update sudo apt-get install libxml2-dev sudo apt-get install r-cran-xml sudo apt-get install libcurl4-openssl-dev Hope it works for you too!

ADD COMMENTlink written 2.4 years ago by csclaros20
1
gravatar for andrew.j.skelton73
3.5 years ago by
London
andrew.j.skelton735.5k wrote:
source("http://bioconductor.org/biocLite.R")

You didn't get an error, it executed. Did you even read the output you pasted here? 

"https:// URLs are not supported by the default method"

secure URLs are not supported by the Source function

"trying "lib curl""

It tries the lib curl library. 

"Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help"

Success. 

Have a go at trying to figure out the errors yourself before posting. Throwing the error into google, plus "R" brings up a number of results. 

ADD COMMENTlink written 3.5 years ago by andrew.j.skelton735.5k

thanks you Andrew,

im trying since morning to install this package, llok at the below please

> source("https://bioconductor.org/biocLite.R")
https:// URLs are not supported by the default method: trying "libcurl"
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite("DESeq2")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.
Installing package(s) ‘DESeq2’
also installing the dependencies ‘stringi’, ‘AnnotationDbi’, ‘stringr’, ‘annotate’, ‘plyr’, ‘reshape2’, ‘scales’, ‘S4Vectors’, ‘Rcpp’, ‘RcppArmadillo’, ‘BiocParallel’, ‘genefilter’, ‘locfit’, ‘geneplotter’, ‘ggplot2’, ‘Hmisc’

trying URL 'http://cran.rstudio.com/src/contrib/stringi_0.5-5.tar.gz'
Content type 'application/x-gzip' length 3639183 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/AnnotationDbi_1.30.1.tar.gz'
Content type 'application/x-gzip' length 4266883 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'http://cran.rstudio.com/src/contrib/stringr_1.0.0.tar.gz'
Content type 'application/x-gzip' length 34880 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/annotate_1.46.1.tar.gz'
Content type 'application/x-gzip' length 1855863 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'http://cran.rstudio.com/src/contrib/plyr_1.8.3.tar.gz'
Content type 'application/x-gzip' length 392337 bytes (383 KB)
==================================================
downloaded 383 KB

trying URL 'http://cran.rstudio.com/src/contrib/reshape2_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34693 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'http://cran.rstudio.com/src/contrib/scales_0.3.0.tar.gz'
Content type 'application/x-gzip' length 57030 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.6.5.tar.gz'
Content type 'application/x-gzip' length 187955 bytes (183 KB)
==================================================
downloaded 183 KB

trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.0.tar.gz'
Content type 'application/x-gzip' length 2297548 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'http://cran.rstudio.com/src/contrib/RcppArmadillo_0.5.500.2.0.tar.gz'
Content type 'application/x-gzip' length 974638 bytes (951 KB)
==================================================
downloaded 951 KB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocParallel_1.2.21.tar.gz'
Content type 'application/x-gzip' length 586398 bytes (572 KB)
==================================================
downloaded 572 KB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/genefilter_1.50.0.tar.gz'
Content type 'application/x-gzip' length 1291651 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'http://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz'
Content type 'application/x-gzip' length 196560 bytes (191 KB)
==================================================
downloaded 191 KB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/geneplotter_1.46.0.tar.gz'
Content type 'application/x-gzip' length 1395872 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'http://cran.rstudio.com/src/contrib/ggplot2_1.0.1.tar.gz'
Content type 'application/x-gzip' length 2351203 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'http://cran.rstudio.com/src/contrib/Hmisc_3.16-0.tar.gz'
Content type 'application/x-gzip' length 629536 bytes (614 KB)
==================================================
downloaded 614 KB

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/DESeq2_1.8.1.tar.gz'
Content type 'application/x-gzip' length 1298105 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/lib64/R
checking for R... /usr/lib64/R/bin/R
checking for R >= 3.1.0... yes
checking for cat... /bin/cat
checking for gcc... gcc -m64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 accepts -g... yes
checking for gcc -m64 option to accept ISO C89... none needed
checking how to run the C preprocessor... g++ -m64 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -m64 -std=c++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /bin/pkg-config
checking with pkg-config for ICU4C installed... 54.1
checking for ICU4C >= 50... yes
checking for proper CPPFLAGS, LDFLAGS, and LIBS... done
checking whether we may build an ICU-based project... yes
checking for available ICU data library (ucnv, uloc, utrans)... yes
checking for available ICU data library (ucol)... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R

*** stringi configure summary:
    ICU_FOUND=1
    ICUDT_DIR=icu55/data
    STRINGI_CXXSTD=CXX_STD=CXX11
    STRINGI_CFLAGS=
    STRINGI_CPPFLAGS=-I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H
    STRINGI_CXXFLAGS=
    STRINGI_LDFLAGS=-L/usr/lib64 
    STRINGI_LIBS=-licui18n -licuuc -licudata 

*** compiler settings used:
    CC=gcc -m64
    CPP=g++ -m64 -E
    LD=g++ -m64
    CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
    CPPFLAGS=-I/usr/local/include  -UDEBUG -DNDEBUG
    CXX=g++ -m64 -std=c++11
    CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
    LDFLAGS=
    LIBS=

** libs
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_brkiter.cpp -o stri_brkiter.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_collator.cpp -o stri_collator.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_common.cpp -o stri_common.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_compare.cpp -o stri_compare.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_base.cpp -o stri_container_base.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_listint.cpp -o stri_container_listint.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_listraw.cpp -o stri_container_listraw.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_listutf8.cpp -o stri_container_listutf8.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_regex.cpp -o stri_container_regex.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_usearch.cpp -o stri_container_usearch.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_utf16.cpp -o stri_container_utf16.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_utf8.cpp -o stri_container_utf8.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_encoding_detection.cpp -o stri_encoding_detection.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_encoding_management.cpp -o stri_encoding_management.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_escape.cpp -o stri_escape.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_exception.cpp -o stri_exception.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_ICU_settings.cpp -o stri_ICU_settings.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_join.cpp -o stri_join.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_length.cpp -o stri_length.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_pad.cpp -o stri_pad.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_prepare_arg.cpp -o stri_prepare_arg.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_random.cpp -o stri_random.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_reverse.cpp -o stri_reverse.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_count.cpp -o stri_search_class_count.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_detect.cpp -o stri_search_class_detect.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_extract.cpp -o stri_search_class_extract.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_locate.cpp -o stri_search_class_locate.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_replace.cpp -o stri_search_class_replace.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_split.cpp -o stri_search_class_split.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_subset.cpp -o stri_search_class_subset.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_class_trim.cpp -o stri_search_class_trim.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_common.cpp -o stri_search_common.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_count.cpp -o stri_search_coll_count.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_split.cpp -o stri_search_coll_split.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_in.cpp -o stri_search_in.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_other_replace.cpp -o stri_search_other_replace.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_other_split.cpp -o stri_search_other_split.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_count.cpp -o stri_search_regex_count.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_match.cpp -o stri_search_regex_match.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_split.cpp -o stri_search_regex_split.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_stats.cpp -o stri_stats.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_stringi.cpp -o stri_stringi.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_sub.cpp -o stri_sub.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_test.cpp -o stri_test.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_time_zone.cpp -o stri_time_zone.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_time_calendar.cpp -o stri_time_calendar.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_time_symbols.cpp -o stri_time_symbols.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_time_format.cpp -o stri_time_format.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_trans_casemap.cpp -o stri_trans_casemap.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_trans_other.cpp -o stri_trans_other.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_trans_normalization.cpp -o stri_trans_normalization.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_ucnv.cpp -o stri_ucnv.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_uloc.cpp -o stri_uloc.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_utils.cpp -o stri_utils.o
g++ -m64 -std=c++11 -I/usr/include/R -DNDEBUG -I.   -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c stri_wrap.cpp -o stri_wrap.o
g++ -m64 -std=c++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_replace.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_stats.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib64 -licui18n -licuuc -licudata -L/usr/lib64/R/lib -lR
installing via 'install.libs.R' to /usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/stringi
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package ‘stringi’
    finding HTML links ...Error in readRDS(f) : error reading from connection
* removing ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/stringi’
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c AEbufs.c -o AEbufs.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c DataFrame_class.c -o DataFrame_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c Hits_class.c -o Hits_class.o
In file included from /usr/include/R/Rdefines.h:29:0,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function ‘Hits_new’:
/usr/include/R/Rinternals.h:1127:20: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define defineVar  Rf_defineVar
                    ^
Hits_class.c:210:12: note: ‘revmap’ was declared here
  SEXP ans, revmap, symbol;
            ^
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c List_class.c -o List_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c Rle_class.c -o Rle_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c Rle_utils.c -o Rle_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c SEXP_utils.c -o SEXP_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c SimpleList_class.c -o SimpleList_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c anyMissing.c -o anyMissing.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c eval_utils.c -o eval_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c hash_utils.c -o hash_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c int_utils.c -o int_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c logical_utils.c -o logical_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c safe_arithm.c -o safe_arithm.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c sort_utils.c -o sort_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c str_utils.c -o str_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c subsetting_internals.c -o subsetting_internals.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c vector_utils.c -o vector_utils.o
gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o subsetting_internals.o vector_utils.o -L/usr/lib64/R/lib -lR
installing to /usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘subset’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘na.omit’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘na.exclude’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘transform’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘by’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘window’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘with’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.table’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘t’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘which’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘mad’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘levels’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘droplevels’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘within’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘S4Vectors’
** help
*** installing help indices
  converting help for package ‘S4Vectors’
    finding HTML links ... done
    Annotated-class                         html 
    DataFrame-class                         html 
    DataTable-class                         html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/DataTable-class.Rd:50: missing file link ‘RangedData’
    Hits-class                              html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Hits-class.Rd:43: missing file link ‘findOverlaps’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Hits-class.Rd:154: missing file link ‘findOverlaps’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Hits-class.Rd:157: file link ‘Hits-examples’ in package ‘IRanges’ does not exist and so has been treated as a topic
    Hits-comparison                         html 
    Hits-setops                             html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Hits-setops.Rd:65: missing file link ‘union’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Hits-setops.Rd:66: missing file link ‘intersect’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Hits-setops.Rd:67: missing file link ‘setdiff’
    List-class                              html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:56: missing file link ‘IntegerList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:70: missing file link ‘IntegerList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:70: missing file link ‘RleList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:71: missing file link ‘RangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:72: missing file link ‘GRangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:76: missing file link ‘GRangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:80: missing file link ‘IntegerList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:81: missing file link ‘RleList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:81: missing file link ‘RangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:91: missing file link ‘CompressedList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:140: missing file link ‘CompressedList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:148: missing file link ‘CompressedList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:211: missing file link ‘IntegerList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:212: missing file link ‘LogicalList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:212: missing file link ‘CharacterList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:213: missing file link ‘RleList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:214: missing file link ‘RleList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:214: missing file link ‘RangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:249: missing file link ‘CompressedList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:252: missing file link ‘IntegerList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:252: missing file link ‘RleList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-class.Rd:253: missing file link ‘IRanges’
    List-utils                              html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:89: missing file link ‘sapply’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:100: missing file link ‘Reduce’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:118: missing file link ‘sapply’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:133: missing file link ‘Reduce’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:157: missing file link ‘Reduce’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:160: missing file link ‘within’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:173: missing file link ‘Reduce’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/List-utils.Rd:176: missing file link ‘within’
    Rle-class                               html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Rle-class.Rd:206: missing file link ‘IRanges’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Rle-class.Rd:380: missing file link ‘aggregate’
    Rle-runstat                             html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Rle-runstat.Rd:91: missing file link ‘RleList-class’
    Rle-utils                               html 
    S4Vectors-internals                     html 
    SimpleList-class                        html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/SimpleList-class.Rd:89: missing file link ‘CompressedList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/SimpleList-class.Rd:93: missing file link ‘SimpleIntegerList’
    Vector-class                            html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Vector-class.Rd:213: missing file link ‘CompressedList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Vector-class.Rd:228: missing file link ‘IRanges’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Vector-class.Rd:228: missing file link ‘XRaw’
    Vector-comparison                       html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Vector-comparison.Rd:277: missing file link ‘Ranges’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/Vector-comparison.Rd:309: missing file link ‘Ranges’
    aggregate-methods                       html 
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:41: missing file link ‘end’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:41: missing file link ‘width’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:45: missing file link ‘RangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:46: missing file link ‘RangesList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:47: missing file link ‘SimpleAtomicList’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:98: missing file link ‘end’
Rd warning: /tmp/Rtmp748VGZ/R.INSTALL6074511b471c/S4Vectors/man/aggregate-methods.Rd:99: missing file link ‘width’
    isSorted                                html 
    str-utils                               html 
    subsetting-internals                    html 
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in readRDS(nsInfoFilePath) : error reading from connection
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/S4Vectors’
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c Date.cpp -o Date.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c Module.cpp -o Module.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c Rcpp_init.cpp -o Rcpp_init.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c api.cpp -o api.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c attributes.cpp -o attributes.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c barrier.cpp -o barrier.o
g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib64/R/lib -lR
installing to /usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package ‘Rcpp’
    finding HTML links ...Error in readRDS(f) : error reading from connection
* removing ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/Rcpp’
* installing *source* package ‘BiocParallel’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package ‘BiocParallel’
    finding HTML links ... done
    BatchJobsParam-class                    html 
    BiocParallel-package                    html 
    BiocParallelParam-class                 html 
    DoparParam-class                        html 
    MulticoreParam-class                    html 
Rd warning: /tmp/Rtmp5I445f/R.INSTALL60de25c9fbfb/BiocParallel/man/MulticoreParam-class.Rd:218: missing file link ‘makeCluster’
    SerialParam-class                       html 
    SnowParam-class                         html 
Rd warning: /tmp/Rtmp5I445f/R.INSTALL60de25c9fbfb/BiocParallel/man/SnowParam-class.Rd:269: missing file link ‘makeCluster’
    bpaggregate                             html 
Rd warning: /tmp/Rtmp5I445f/R.INSTALL60de25c9fbfb/BiocParallel/man/bpaggregate.Rd:47: missing file link ‘simplify2array’
    bpiterate                               html 
    bplapply                                html 
    bpmapply                                html 
Rd warning: /tmp/Rtmp5I445f/R.INSTALL60de25c9fbfb/BiocParallel/man/bpmapply.Rd:46: missing file link ‘simplify2array’
    bpok                                    html 
    bpschedule                              html 
    bpvalidate                              html 
    bpvec                                   html 
    bpvectorize                             html 
    register                                html 
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocParallel)
* installing *source* package ‘locfit’ ...
** package ‘locfit’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c S_enter.c -o S_enter.o
S_enter.c: In function ‘sfitted’:
S_enter.c:445:11: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
 { Sint i, n;
           ^
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c band.c -o band.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c dbinom.c -o dbinom.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c dens_haz.c -o dens_haz.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c dens_int.c -o dens_int.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c dens_odi.c -o dens_odi.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c density.c -o density.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c ev_atree.c -o ev_atree.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c ev_interp.c -o ev_interp.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c ev_kdtre.c -o ev_kdtre.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c ev_main.c -o ev_main.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c ev_sphere.c -o ev_sphere.o
ev_sphere.c: In function ‘sphere_start’:
ev_sphere.c:24:7: warning: variable ‘d’ set but not used [-Wunused-but-set-variable]
 { int d, i, j, ct, nv, ncm, vc, *mg;
       ^
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c ev_trian.c -o ev_trian.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune

but at last when i tried to call the package it told:* preparing package for lazy loading
Error : package ‘BSgenome’ 1.32.0 was found, but >= 1.33.5 is required by ‘BSgenome.Celegans.UCSC.ce2’
ERROR: lazy loading failed for package ‘BSgenome.Celegans.UCSC.ce2’
* removing ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/BSgenome.Celegans.UCSC.ce2’

The downloaded source packages are in
    ‘/tmp/RtmpkCfwfZ/downloaded_packages’
There were 50 or more warnings (use warnings() to see the first 50)
> install.packages("DESeq2")
Installing package into ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘DESeq2’ is not available (for R version 3.2.1)
> install.packages("DESeq2")
Installing package into ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘DESeq2’ is not available (for R version 3.2.1)

 

 

ADD REPLYlink written 3.5 years ago by F3.4k
1

This is your problem:

Error : package ‘BSgenome’ 1.32.0 was found, but >= 1.33.5 is required by ‘BSgenome.Celegans.UCSC.ce2’

The package you are trying to install or its dependencies needs a newer version of this BSgenome. You probably had an earlier version already installed. 

Try updating it first

biocLite("BSgenome")

then 

biocLite("DESeq2")

 

 

ADD REPLYlink written 3.5 years ago by Lemire380

thank you

i will try

ADD REPLYlink written 3.5 years ago by F3.4k

run

biocLite()

to update all your outdated packages then

biocLite("DESeq2")

The install.packages function is for CRAN libraries, whereas DESeq2 is a Bioconductor Library. 

ADD REPLYlink written 3.5 years ago by andrew.j.skelton735.5k

sorry Andrew,

i did what you said

but asked me Would you like to use a personal library instead?  (y/n) and i typed y and after some time said that:

The downloaded source packages are in
    ‘/tmp/RtmpzRdBqS/downloaded_packages’
There were 50 or more warnings (use warnings() to see the first 50)
>

now from where i can recognize that if the package installed or not?

thank you

ADD REPLYlink written 3.5 years ago by F3.4k
1
library(DESeq2)
ADD REPLYlink written 3.5 years ago by andrew.j.skelton735.5k

> library(DESeq2)
Error in library(DESeq2) : there is no package called ‘DESeq2’
> :(

then what can i do now?

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by F3.4k
1

Did you run 

warnings()

As it suggested?

ADD REPLYlink written 3.5 years ago by andrew.j.skelton735.5k

hi andrew,

this is my 50 error

There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Biostrings’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Rsamtools’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘BRugs’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘IRanges’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘qtl’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘RODBC’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘SparseM’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘spatial’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘survival’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘tree’ had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘XML’ had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘affy’ had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘caTools’ had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘class’ had non-zero exit status
18: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘maanova’ had non-zero exit status
19: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Matrix’ had non-zero exit status
20: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘multtest’ had non-zero exit status
21: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘nlme’ had non-zero exit status
22: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘RCurl’ had non-zero exit status
23: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘sp’ had non-zero exit status
24: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘XVector’ had non-zero exit status
25: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Biostrings’ had non-zero exit status
26: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘GenomicRanges’ had non-zero exit status
27: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘mgcv’ had non-zero exit status
28: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘rgdal’ had non-zero exit status
29: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rsamtools’ had non-zero exit status
30: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘GenomicAlignments’ had non-zero exit status
31: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘rtracklayer’ had non-zero exit status
32: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘nloptr’ had non-zero exit status
33: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘stringi’ had non-zero exit status
34: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rcpp’ had non-zero exit status
35: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘affydata’ had non-zero exit status
36: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘ALL’ had non-zero exit status
37: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘BiocGenerics’ had non-zero exit status
38: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘DBI’ had non-zero exit status
39: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘fibroEset’ had non-zero exit status
40: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘pls’ had non-zero exit status
41: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘qcc’ had non-zero exit status
42: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘RUnit’ had non-zero exit status
43: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘sandwich’ had non-zero exit status
44: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘statmod’ had non-zero exit status
45: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘TH.data’ had non-zero exit status
46: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘timeDate’ had non-zero exit status
47: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘widgetTools’ had non-zero exit status
48: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘xtable’ had non-zero exit status
49: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘minqa’ had non-zero exit status
50: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘RcppEigen’ had non-zero exit status
>

 

ADD REPLYlink written 3.5 years ago by F3.4k

As @Lemire/OICR stated, from your original log:

Error : package ‘BSgenome’ 1.32.0 was found, but >= 1.33.5 is required by ‘BSgenome.Celegans.UCSC.ce2’

Is the issue, you need to install an updated version. 

ADD REPLYlink written 3.5 years ago by andrew.j.skelton735.5k

thank you,

i did the same but again the same question(would you like to your personal file) i typed y but

Error : package ‘BSgenome’ 1.32.0 was found, but >= 1.33.5 is required by ‘BSgenome.Celegans.UCSC.ce2’
ERROR: lazy loading failed for package ‘BSgenome.Celegans.UCSC.ce2’
* removing ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/BSgenome.Celegans.UCSC.ce2’

The downloaded source packages are in
    ‘/tmp/Rtmpwnc0IZ/downloaded_packages’
There were 50 or more warnings (use warnings() to see the first 50)
> library(DESeq2)
Error in library(DESeq2) : there is no package called ‘DESeq2’
> library(/usr/data/nfs6/izadi/R-3.2.2/lib/DESeq2)
Error: unexpected '/' in "library(/"

ADD REPLYlink written 3.5 years ago by F3.4k

You ran

biocLite("BSgenome")

didn't you?

ADD REPLYlink written 3.5 years ago by andrew.j.skelton735.5k

i ran biocLite("BSgenome") the first then i ran (DESeq2)...but the same error...there is a file named R-3.2.2 in /usr/data/nfs6/izadi/ containing many folders then i ran the library(/usr/data/nfs6/izadi/R-3.2.2/lib/DESeq2) but agsin error...totally i donno how i can install this package

ADD REPLYlink written 3.5 years ago by F3.4k
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