Question: Error in installation R package
0
gravatar for niutster
2.9 years ago by
niutster80
niutster80 wrote:

Hi, I am trying to install "minfi" package with these commamnds: source("https://bioconductor.org/biocLite.R") biocLite("minfi"), but when R starts to install RSQLite package on Ubuntu workstation, i get this error: ERROR: compilation failed for package 'RSQLite'. R version is 3.2.3.

How can i solve it?

R • 4.3k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 2.9 years ago by niutster80

Can you post the full error message? It should mention why it failed.

ADD REPLYlink written 2.9 years ago by igor8.0k

make: * [fetch.o] Error 1 ERROR: compilation failed for package 'RSQLite' R version 3.2.3

ADD REPLYlink written 2.9 years ago by niutster80
fetch.c: In function 'rsqlite_output_alloc':
fetch.c:25:3: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
   for (int j = 0; j < p; j++) {
   ^
fetch.c:25:3: note: use option -std=c99, -std=gnu99, -std=c11 or -std=gnu11 to compile your code
fetch.c:32:12: error: redefinition of 'j'
   for (int j = 0; j < p; j++) {
            ^
fetch.c:25:12: note: previous definition of 'j' was here
   for (int j = 0; j < p; j++) {
            ^
fetch.c:32:3: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
   for (int j = 0; j < p; j++) {
   ^
fetch.c: In function 'rsqlite_output_expand':
fetch.c:44:3: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
   for (int j = 0; j < p; j++) {
   ^
fetch.c: In function 'fill_one_row':
fetch.c:251:3: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
   for (int j = 0; j < flds->num_fields; j++) {
   ^
fetch.c: In function 'rsqlite_query_fetch':
fetch.c:381:5: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
     for (int j = 0; j < num_fields; j++) {
     ^
make: *** [fetch.o] Error 1
ERROR: compilation failed for package 'RSQLite'
* removing '/home/barjaste/R/x86_64-pc-linux-gnu-library/3.2/RSQLite'
* installing *source* package 'openssl' ...
ADD REPLYlink modified 2.9 years ago by genomax70k • written 2.9 years ago by niutster80

I assume it's the same when you try install.packages("RSQLite")? Do you have an outdated compiler? (Check with gcc --version in a terminal.

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k

I checked it:

gcc (GCC) 4.9.0 Copyright (C) 2014 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

ADD REPLYlink written 2.9 years ago by niutster80

Can you check install.packages('openssl')? I think that's the culprit. If it fails, please post the complete error message.

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k

I have downloaded openssl from https://cran.r-project.org/web/packages/openssl/index.html and installed it with this command : install.packages("/home/barjaste/openssl_0.9.4.tgz",repos=NULL,source="type") Installing package into '/home/barjaste/R/x86_64-pc-linux-gnu-library/3.2' (as 'lib' is unspecified) * installing binary package 'openssl' ... * DONE (openssl)

require(openssl) Loading required package: openssl Failed with error: 'package 'openssl' was built for x86_64-apple-darwin13.4.0' In addition: Warning message: package 'openssl' was built under R version 3.2.5

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by niutster80

It sounds that the problem is for bioconductor packages not for CRAN packages.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by niutster80

Why do you manually download the package and install it then? Just run install.packages('openssl') in R terminal... Could you try with installing libssl-dev first: sudo apt-get install libssl-dev

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k

At first, this massage appears:

Installing package into '/home/barjaste/R/x86_64-pc-linux-gnu-library/3.2' (as 'lib' is unspecified) --- Please select a CRAN mirror for use in this session --- Error in download.file(url, destfile = f, quiet = TRUE) : unsupported URL scheme HTTPS CRAN mirror

1: 0-Cloud [https] 2: Austria [https] 3: Chile [https] 4: China (Beijing 4) [https] 5: Colombia (Cali) [https] 6: France (Lyon 2) [https] 7: France (Paris 2) [https] 8: Germany (M▒nster) [https] 9: Iceland [https] 10: Mexico (Mexico City) [https] 11: Russia (Moscow) [https] 12: Spain (A Coru▒a) [https] 13: Switzerland [https] 14: UK (Bristol) [https] 15: UK (Cambridge) [https] 16: USA (CA 1) [https] 17: USA (KS) [https] 18: USA (MI 1) [https] 19: USA (TN) [https] 20: USA (TX) [https] 21: USA (WA) [https] 22: (HTTP mirrors)

after selection, it says Selection: 1 Warning: unable to access index for repository https://cran.rstudio.com/src/contrib: unsupported URL scheme Warning message: package 'openssl' is not available (for R version 3.2.3)

When i tried for the second time, it says:

Installing package into '/home/barjaste/R/x86_64-pc-linux-gnu-library/3.2' (as 'lib' is unspecified) Warning: unable to access index for repository https://cran.rstudio.com/src/contrib: unsupported URL scheme Warning message: package 'openssl' is not available (for R version 3.2.3)

install.packages('openssl') Installing package into '/home/barjaste/R/x86_64-pc-linux-gnu-library/3.2' (as 'lib' is unspecified) Warning: unable to access index for repository https://cran.rstudio.com/src/contrib: unsupported URL scheme Warning message: package 'openssl' is not available (for R version 3.2.3)

ADD REPLYlink written 2.9 years ago by niutster80

For the second command:

sudo apt-get install libssl-dev Error: unexpected symbol in "sudo apt"

ADD REPLYlink written 2.9 years ago by niutster80
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