Problems installing BiocLite on Fedora 23, R 3.2.2
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Knut Hansen ▴ 20
@knut-hansen-5605
Last seen 5.8 years ago
Norway

I'm running Fedora 23 with KDE 5.16. I'm trying to install biocLite using the commands

source("https://bioconductor.org/biocLite.R")
biocLite()

as root.

After answering 'a' to the question on which packages I want to install, I get the following (edited) output:

* installing *source* package ‘base64enc’ ...

** package ‘base64enc’ 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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c base64.c -o base64.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
/usr/lib64/R/etc/Makeconf:134: recipe for target 'base64.o' failed
make: *** [base64.o] Error 1
ERROR: compilation failed for package ‘base64enc’
* removing ‘/usr/lib64/R/library/base64enc’
* restoring previous ‘/usr/lib64/R/library/base64enc’
* installing *source* package ‘Biobase’ ...

Same errors with packages:

base64enc’,‘Biobase’,‘checkmate’,‘colorspace’,‘digest’,‘foreign’,‘illuminaio’,‘jsonlite’,‘limma’,‘MASS’,‘matrixStats’,‘mclust’,‘mime’,‘nleqslv’,‘nlme’,‘nnet’,‘preprocessCore’,‘Rcpp’,‘RCurl’,‘RSQLite’,‘
S4Vectors’,‘setwidth’,‘spatial’,‘XML’,‘zlibbioc’,‘affyio’,‘BBmisc’,‘class’,‘genefilter’,‘httpuv’,‘IRanges’,‘mgcv’,‘minqa’,‘multtest’,‘plyr’,‘RcppEigen’,‘affy’,‘GenomeInfoDb’,‘lme4’,‘scales’,‘shiny’,‘XVe
ctor’,‘Biostrings’,‘GenomicRanges’,‘Rsamtools’,‘S4Vectors’,‘GenomeInfoDb’.

I have tried to reinstall gcc to no avail. Does anyone have a solution or work around?

Output from sessioninfo() is:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 23 (Workstation Edition)

locale:
[1] LC_CTYPE=nb_NO.UTF-8       LC_NUMERIC=C               
[3] LC_TIME=nb_NO.UTF-8        LC_COLLATE=nb_NO.UTF-8     
[5] LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=nb_NO.UTF-8    
[7] LC_PAPER=nb_NO.UTF-8       LC_NAME=C                  
[9] LC_ADDRESS=C               LC_TELEPHONE=C             
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C        

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base      

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.2

 

Knut Hansen
University of Tromsø

bioclite gcc install fedora • 1.8k views
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@martin-morgan-1513
Last seen 10 weeks ago
United States

I might have been a little hasty to forward you here from R-help, because you mentioned biocLite and Rsamtools. It looks like, in addition to Bioconductor-specific problems that you are likely to run into with Rsamtools, there is a basic system configuration issue. I am not sure exactly how, but you want to arrange to install redhat-hardened-cc1 on your system. I have no more direct experience than google, which suggests yum install redhat-rpm-config.

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Thank you, that got me a bit further. All packages now installed with quite a few warnings, but no errors. My ultimate goal, however, is to install the "lumi" package under R v. 3.2.2. Now, biocLite('lumi') will install this package to without errors, but with some warnings. But when I try to load it with library(lumi) or library('lumi') I get the errors:

Error : Functions found when exporting methods from the namespace ‘S4Vectors’ which are not S4 generic: ‘grep’, ‘grepl’, ‘subset’
Error: package or namespace load failed for ‘lumi’
 

Googling a bit I found a suggestion for a similar problem where someone was advised to install the package 'BioGenerics'. However this package does not exist for R 3.2.2. I have also done a update.packages() without any luck.

Knut H.

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The package you would have been advised to install is 'BiocGenerics' (note the 'c').

A final step in package installation is to test the the installed package loads, so at the time of installation your libraries were configured successfully.

Verify that packageVersion("BiocInstaller") reports 1.20.1.

Does BiocInstaller::biocValid() report version mis-matches between packages? If so, try and resolve those. If there are 'warnings' that indicate that package(s) fail to install, 'drill down' to isolate the first package that fails to install, and trouble-shoot or provide the complete output of the attempt to install that package.

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Yes I did install biocGenerics, just an error in my post.

BiocInstaller is v. 1.20.1, but there were 25 packages with version mismatch. Fixing that BiocInstaller::biocValid() now reports TRUE.

But my problem now seems to be permissions. I have installed all packages as root. When I try to do library('lumi') as root it works perfectly, but when I do it as an ordinary user I still get the namespace errors. So now I go hunting for wrong file permissions. Any suggestion for candidates is appreciated!

Knut H.

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As root I guess you have entries in .libPaths() that are different from entries in user .libPaths(). Likely the user account has a version of BiocGenerics / S4Vectors in their .libPaths() different from root. File permissions per se should not be a problem.

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You were absolutely right. Now it works!

Thank you!

Knut H.

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