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INSTALL report for CGEN on malbec1

This page was generated on 2020-08-10 11:34:36 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CGEN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 255/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 3.25.1
William Wheeler
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/CGEN
Branch: master
Last Commit: adf5934
Last Changed Date: 2020-06-01 09:59:32 -0400 (Mon, 01 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  ERROR 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: CGEN
Version: 3.25.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CGEN
StartedAt: 2020-08-09 16:08:17 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 16:08:40 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 23.7 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CGEN
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CGEN’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Additive.c -o Additive.o
Additive.c: In function ‘compute_g’:
Additive.c:233:19: warning: ‘et22’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
              ~~~~~^~~~~~
Additive.c:235:25: warning: ‘t22’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
              ~~~~~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CML.c -o CML.o
CML.c:132:13: warning: ‘print_dVec’ defined but not used [-Wunused-function]
 static void print_dVec(vec, n, name)
             ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ccl.c -o ccl.o
ccl.c:386:13: warning: ‘tree_print’ defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^~~~~~~~~~
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c csclust.f -o csclust.o
f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs]
f951: Warning: Nonconforming tab character in column 2 of line 190 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs]
csclust.f:222:3:

 650   RETURN
   1
Warning: Label 650 at (1) defined but not used [-Wunused-label]
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fsclust.c -o fsclust.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hcl.c -o hcl.o
hcl.c:375:13: warning: ‘tree_print’ defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pmatch.c -o pmatch.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c score.c -o score.o
score.c: In function ‘infoSmallStandard’:
score.c:18:27: warning: unused variable ‘ii’ [-Wunused-variable]
   int  nr, nc, i, j, row, ii, nc2;
                           ^~
score.c: In function ‘getScoreEB’:
score.c:183:21: warning: unused variable ‘p6’ [-Wunused-variable]
   double *p4, *p5, *p6;
                     ^~
score.c:183:16: warning: unused variable ‘p5’ [-Wunused-variable]
   double *p4, *p5, *p6;
                ^~
score.c:183:11: warning: unused variable ‘p4’ [-Wunused-variable]
   double *p4, *p5, *p6;
           ^~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-CGEN/00new/CGEN/libs
** R
** data
** 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 from temporary location
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (CGEN)