Question: trouble in install DESeq2
0
gravatar for yueli7
13 months ago by
yueli70
China
yueli70 wrote:

Hello,

 

I have trouble in install the package DESeq2.

 

Thank you in advance!

 

 /home/administrator/R/x86_64-pc-linux-gnu-library/3.2/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help

gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agexact.c -o agexact.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agfit4.c -o agfit4.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agfit5.c -o agfit5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agmart.c -o agmart.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agmart2.c -o agmart2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agmart3.c -o agmart3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agscore.c -o agscore.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agsurv3.c -o agsurv3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agsurv4.c -o agsurv4.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c agsurv5.c -o agsurv5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c chinv2.c -o chinv2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c chinv3.c -o chinv3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cholesky2.c -o cholesky2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cholesky3.c -o cholesky3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cholesky5.c -o cholesky5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c chsolve2.c -o chsolve2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c chsolve3.c -o chsolve3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c chsolve5.c -o chsolve5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c concordance1.c -o concordance1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cox_Rcallback.c -o cox_Rcallback.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxcount1.c -o coxcount1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxdetail.c -o coxdetail.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxexact.c -o coxexact.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxfit5.c -o coxfit5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxfit6.c -o coxfit6.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxmart.c -o coxmart.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxmart2.c -o coxmart2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxph_wtest.c -o coxph_wtest.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxsafe.c -o coxsafe.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxscho.c -o coxscho.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coxscore.c -o coxscore.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dmatrix.c -o dmatrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c doloop.c -o doloop.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c finegray.c -o finegray.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gchol.c -o gchol.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pyears1.c -o pyears1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pyears2.c -o pyears2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pyears3b.c -o pyears3b.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pystep.c -o pystep.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survConcordance.c -o survConcordance.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survdiff2.c -o survdiff2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survfit4.c -o survfit4.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survfitci.c -o survfitci.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survpenal.c -o survpenal.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survreg6.c -o survreg6.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survreg7.c -o survreg7.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survregc1.c -o survregc1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survregc2.c -o survregc2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c survsplit.c -o survsplit.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tmerge.c -o tmerge.o
gcc -std=gnu99 -shared -L/usr/local/lib -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o
installing to /home/administrator/R/x86_64-pc-linux-gnu-library/3.2/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)

The downloaded source packages are in
    ‘/tmp/Rtmp5Ild1V/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status
> BiocInstaller::biocValid()
[1] TRUE
> traceback()
2: stop(txt, domain = NA)
1: library("DESeq2")
> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

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

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

other attached packages:
[1] XML_3.98-1.11        BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.2.5


 

ADD COMMENTlink modified 13 months ago • written 13 months ago by yueli70

So sorry about that: I write in the wrong place.

 

 

Thank you so much!

 

I try to use R-3.5.0, but it is still old version.

What can I do!

 

Thank you in advance!

 

administrator@ACB-HuangLab-Ubuntu:~$ cd R-3.5.0/
administrator@ACB-HuangLab-Ubuntu:~/R-3.5.0$ R

R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


 

ADD REPLYlink modified 13 months ago • written 13 months ago by yueli70
Answer: trouble in install DESeq2
2
gravatar for Michael Love
13 months ago by
Michael Love24k
United States
Michael Love24k wrote:

I don't see the error in the above R output -- I'm assuming this is the end of biocLite("DESeq2")?

Note: your R version is 2 years old, if you're starting a new project, why not use the latest version?

ADD COMMENTlink written 13 months ago by Michael Love24k

Thank you so much!

 

I try to use R-3.5.0, but it is still old version.

What can I do!

 

Thank you in advance!

 

 

administrator@ACB-HuangLab-Ubuntu:~$ cd R-3.5.0/
administrator@ACB-HuangLab-Ubuntu:~/R-3.5.0$ R

R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


 

ADD REPLYlink written 13 months ago by yueli70

Thank you again!

I tried another way.

 

administrator@ACB-HuangLab-Ubuntu:~$ cd R-3.5.0/bin
administrator@ACB-HuangLab-Ubuntu:~/R-3.5.0/bin$ R

R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


 

ADD REPLYlink written 13 months ago by yueli70

Thank you so much!

 

I have fixed it.

make install

 

administrator@ACB-HuangLab-Ubuntu:~$ R

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


 

ADD REPLYlink written 13 months ago by yueli70
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