unable to update mgcv package
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@mail2vignesh1985-9422
Last seen 5.8 years ago

HI,

I would like to install SNPRelate package but it dependent  package 'mgcv' need to be update. it shows following error.  i tried deleting library and reinstalling. But nothing works. Even i update R latest version (R version 3.2.3 (2015-12-10)). 

####

/usr/bin/ld: cannot find -lgfortran

collect2: error: ld returned 1 exit status
make: *** [mgcv.so] Error 1
ERROR: compilation failed for package ‘mgcv’
* removing ‘/usr/lib/R/library/mgcv’
* restoring previous ‘/usr/lib/R/library/mgcv’

The downloaded source packages are in
        ‘/tmp/RtmpQvLZ1S/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘mgcv’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘mgcv’ had non-zero exit status

######

my sessioninfo is 

######

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.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_3.2.3

#####

 

mgcv snprelate • 5.0k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

Try:

​sudo apt-get install gfortran

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I have newest version of gfortran for Ubuntu 12.04. 

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zhengx ▴ 30
@zhengx-7950
Last seen 2.1 years ago
United States

See: https://github.com/zhengxwen/SNPRelate/issues/2, you might have to modify R Makeconf file which is in the folder of R lib.

 

 

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@martin-morgan-1513
Last seen 10 weeks ago
United States

Make sure that libgfortran is in the ldconfig path; I have

$ ldconfig -p|grep gfortran
    libgfortran.so.3 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libgfortran.so.3

The steps to make this so are (a) to install libgfortran (sounds like this is the case), (b) update ldconfig (google is your friend), but this requires sudo (the ldconfig content would normally be updated as part of a typical installation of libgfortran), or if (b) is not possible then (c) add the LD_LIBRARY_PATH environment variable to point to the folder that contains libgfortran.so.

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Hi Martin,

I have checked everything you have written here, including an updated R version (3.4.1), as well as Bioconductor (3.5), and I am still receiving the same error... I am trying to do some ChIp analysis, and all other packages require that "ChIPpeakAnno" be installed properly.. I receive the following error message when I try to install the following packages: "RMySQL", "ReactomePA", "BiocParallel", "motifRG"..

Here is the error message.

______________________________________________________________________________________________________

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
Installing package(s) 'motifRG'
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/motifRG_1.20.0.tar.gz'
Content type 'application/x-gzip' length 1133451 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘motifRG’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifRG)

The downloaded source packages are in
    '/tmp/RtmpiVDKIq/downloaded_packages'
Old packages: 'ChIPpeakAnno'
Update all/some/none? [a/s/n]:
a
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/ChIPpeakAnno_3.10.1.tar.gz'
Content type 'application/x-gzip' length 17012914 bytes (16.2 MB)
==================================================
downloaded 16.2 MB

* installing *source* package ‘ChIPpeakAnno’ ...
mv: cannot move '/home/rtg/R/x86_64-pc-linux-gnu-library/3.4/ChIPpeakAnno' to '/home/rtg/R/x86_64-pc-linux-gnu-library/3.4/00LOCK-ChIPpeakAnno/ChIPpeakAnno': Permission denied
Warning in file.copy(f, instdir, TRUE) :
  problem copying ./NAMESPACE to /home/rtg/R/x86_64-pc-linux-gnu-library/3.4/ChIPpeakAnno/NAMESPACE: Permission denied
Warning in file(file, if (append) "a" else "w") :
  cannot open file '/home/rtg/R/x86_64-pc-linux-gnu-library/3.4/ChIPpeakAnno/DESCRIPTION': Permission denied
Error in file(file, if (append) "a" else "w") :
  cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘ChIPpeakAnno’
* removing ‘/home/rtg/R/x86_64-pc-linux-gnu-library/3.4/ChIPpeakAnno’

The downloaded source packages are in
    '/tmp/RtmpiVDKIq/downloaded_packages'
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package 'ChIPpeakAnno' had non-zero exit status

_____________________________________________________________

session info:

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

___________________________________________________________________________________________________-

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Use your operating system to look in /home/rtg/R/x86_64-pc-linux-gnu-library/3.4/ and make sure that the user you are running as has access to the directories mentioned in the failed installation.

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OK. I will check, I have looked at other support pages, and ran some tests using sudo update package_install.. etc. 

Thanks!

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It shouldn't be as fancy as that, and you shouldn't be doing things with sudo (except installing system libraries). I'd guess that some directories under /home/rtg/R/x86_64-pc-linux-gnu-library/3.4/ are owned by root, and they definitely should not be. You'd need to use sudo to remove them or to chown to your user, but that's it.

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It turns out the issue was that the ChIPpeakAnno package was locked, so I couldn't make any changes, and I also turned off the "syncing" of Dropbox when I installed the package...and this worked

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