Question: Error in loading R package "hgu133a.db"
1
gravatar for zaynabmousavian
4.4 years ago by
zaynabmousavian10 wrote:

Hi,

I have installed the R package "hgu133a.db" successfully, but when I want to load this package, I have gotten the following error:

> library("hgu133a.db")
Loading required package: org.Hs.eg.db
Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error: package ‘org.Hs.eg.db’ could not be loaded

Could anyone help me to resolve this problem?

Best Regards

 

 

 

R • 6.0k views
ADD COMMENTlink modified 4.4 years ago by petr10 • written 4.4 years ago by zaynabmousavian10

is

"org.Hs.eg.db" %in% installed.packages()

?

ADD REPLYlink written 4.4 years ago by russhh4.3k

Yes, this package is also installed.

ADD REPLYlink written 4.4 years ago by zaynabmousavian10
1
gravatar for petr
4.4 years ago by
petr10
Spain
petr10 wrote:

I am experiencing exactly the same problem - for me the following packages are broken / do not load:

GO.db

org.Hs.eg.db

And probably others.

 

EDIT:

Found that the problem is caused with RSQLite version 1.0.0, which is not backwards-compatible.

You can go to your R library folder (see

.libPaths()
and issue following:

wget https://github.com/rstats-db/RSQLite/archive/0.11.4.tar.gz
Rscript -e "install.packages('0.11.4.tar.gz', repos=NULL)"

This would go to github and download older version of RSQLite. Make sure you say NO to any further bioconductor prompts to upgrade packages!

Further information: https://support.bioconductor.org/p/62796/

 

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by petr10

Can you resolve it?

ADD REPLYlink written 4.4 years ago by zaynabmousavian10

see my update!

ADD REPLYlink written 4.4 years ago by petr10

I don't understand properly what I do?

Download the oldest version of RSQLite from this url in the path of .libPaths() and then run the following commands:

setwd(.libPaths())

install.packages('0.11.4.tar.gz', repos=NULL)

Is this true?

ADD REPLYlink written 4.4 years ago by zaynabmousavian10

I've done it on unix-based machine, but your steps are probably the same.

Instead of the Rscript in the commandline, just run R and provide full path to the install.packages command:

install.packages('full/path/to0.11.4.tar.gz', repos=NULL)
ADD REPLYlink written 4.4 years ago by petr10

I have tried to install package, but I get the following error:

> install.packages("RSQLite-0.11.4.tar.gz", repos=NULL,type="source")
Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package 'RSQLite' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m32 -I"C:/PROGRA~1/R/R-30~1.3/include" -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000 -DSQLITE_MAX_COLUMN=30000    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RS-DBI.c -o RS-DBI.o
gcc: unrecognized option `-std=gnu99'
cc1.exe: Invalid option `32'
cc1.exe: Invalid option `tune=core2'
RS-DBI.c: In function `DBI_handle_to_string':
RS-DBI.c:1215: warning: implicit declaration of function `snprintf'
make.exe: *** [RS-DBI.o] Error 1
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-30~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-30~1.3/share/make/winshlib.mk" SHLIB="RSQLite.dll" OBJECTS="RS-DBI.o RS-SQLite.o param_binding.o sqlite-all.o"' had status 2
ERROR: compilation failed for package 'RSQLite'
* removing 'C:/Program Files/R/R-3.0.3/library/RSQLite'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-30~1.3/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.3\library" "RSQLite-0.11.4.tar.gz"' had status 1 
2: In install.packages("RSQLite-0.11.4.tar.gz", repos = NULL, type = "source") :
  installation of package ‘RSQLite-0.11.4.tar.gz’ had non-zero exit status
 

 

 

ADD REPLYlink written 4.4 years ago by zaynabmousavian10

I have tried to install package, but I get the following error:

> install.packages("RSQLite-0.11.4.tar.gz", repos=NULL,type="source")
Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package 'RSQLite' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m32 -I"C:/PROGRA~1/R/R-30~1.3/include" -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000 -DSQLITE_MAX_COLUMN=30000    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RS-DBI.c -o RS-DBI.o
gcc: unrecognized option `-std=gnu99'
cc1.exe: Invalid option `32'
cc1.exe: Invalid option `tune=core2'
RS-DBI.c: In function `DBI_handle_to_string':
RS-DBI.c:1215: warning: implicit declaration of function `snprintf'
make.exe: *** [RS-DBI.o] Error 1
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-30~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-30~1.3/share/make/winshlib.mk" SHLIB="RSQLite.dll" OBJECTS="RS-DBI.o RS-SQLite.o param_binding.o sqlite-all.o"' had status 2
ERROR: compilation failed for package 'RSQLite'
* removing 'C:/Program Files/R/R-3.0.3/library/RSQLite'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-30~1.3/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.3\library" "RSQLite-0.11.4.tar.gz"' had status 1 
2: In install.packages("RSQLite-0.11.4.tar.gz", repos = NULL, type = "source") :
  installation of package ‘RSQLite-0.11.4.tar.gz’ had non-zero exit status
 

 

 

ADD REPLYlink written 4.4 years ago by zaynabmousavian10

I could install the RSQLite package successfully by converting .tar.gz file to a .zip file, but my problem about loading package "hgu133a.db" is also remained!

ADD REPLYlink written 4.4 years ago by zaynabmousavian10

I could install the RSQLite package successfully by converting .tar.gz file to a .zip file, but my problem about loading package "hgu133a.db" is also remained!

ADD REPLYlink written 4.4 years ago by zaynabmousavian10

I am not sure if you're completely set-up to compile packages from source... or maybe the procedure is different on windows system - not sure!

ADD REPLYlink written 4.4 years ago by petr10

My OS is windows!

ADD REPLYlink written 4.4 years ago by zaynabmousavian10
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