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This page was generated on 2024-02-28 11:36:20 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1730/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rGADEM 2.50.0  (landing page)
Arnaud Droit
Snapshot Date: 2024-02-27 14:05:07 -0500 (Tue, 27 Feb 2024)
git_url: https://git.bioconductor.org/packages/rGADEM
git_branch: RELEASE_3_18
git_last_commit: 2ec7aeb
git_last_commit_date: 2023-10-24 09:43:19 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for rGADEM on nebbiolo2


To the developers/maintainers of the rGADEM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rGADEM.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rGADEM
Version: 2.50.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL rGADEM
StartedAt: 2024-02-27 15:15:52 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 15:16:36 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 44.1 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL rGADEM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘rGADEM’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for gcc option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking whether OpenMP will work in a package... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function ‘GADEM_Analysis’:
Gadem_Analysis.c:274:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  274 |   for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
      |   ^~~
Gadem_Analysis.c:274:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  274 |   for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
      |                                                   ^~~~~~~~~
Gadem_Analysis.c:182:59: warning: variable ‘totalSitesInput’ set but not used [-Wunused-but-set-variable]
  182 |   int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput;
      |                                                           ^~~~~~~~~~~~~~~
Gadem_Analysis.c:174:7: warning: variable ‘generationNoMotif’ set but not used [-Wunused-but-set-variable]
  174 |   int generationNoMotif;                 // maximal number of GA generations in a GADEM cycle resulted in no motifs
      |       ^~~~~~~~~~~~~~~~~
Gadem_Analysis.c:113:12: warning: variable ‘logepwm’ set but not used [-Wunused-but-set-variable]
  113 |   double **logepwm;                      // log(em-optimized PWM)
      |            ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c align_sites.c -o align_sites.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c alloc.c -o alloc.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c background.c -o background.o
background.c: In function ‘count_nucleotides’:
background.c:818:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  818 |          for (k=0; k<wordLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
background.c:818:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  818 |          for (k=0; k<wordLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                       ^~
background.c:826:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  826 |          for (k=0; k<wordLen; k++) s1[k]=rseq[i][j+k]; s1[k]='\0';
      |          ^~~
background.c:826:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  826 |          for (k=0; k<wordLen; k++) s1[k]=rseq[i][j+k]; s1[k]='\0';
      |                                                        ^~
background.c: In function ‘ll_score_backg_model’:
background.c:1104:10: warning: variable ‘s1’ set but not used [-Wunused-but-set-variable]
 1104 |    char *s1;
      |          ^~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c base_frequency.c -o base_frequency.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c check_convergence.c -o check_convergence.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c check_pwm_dist.c -o check_pwm_dist.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c consensus.c -o consensus.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c construct_pwm.c -o construct_pwm.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c copy_pwm.c -o copy_pwm.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c crossover.c -o crossover.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c effect_seq_len.c -o effect_seq_len.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c evalue_meme.c -o evalue_meme.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c extend_alignment.c -o extend_alignment.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c initial_population.c -o initial_population.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c mask_sites.c -o mask_sites.o
mask_sites.c: In function ‘mask_repetitive’:
mask_sites.c:61:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   61 |       for (k=0,i=id+1; i<strlen(fileName); i++,k++) maskedFileName[k]=fileName[i]; maskedFileName[k]='\0';
      |       ^~~
mask_sites.c:61:84: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   61 |       for (k=0,i=id+1; i<strlen(fileName); i++,k++) maskedFileName[k]=fileName[i]; maskedFileName[k]='\0';
      |                                                                                    ^~~~~~~~~~~~~~
mask_sites.c:69:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   69 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
mask_sites.c:69:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   69 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                    ^~
mask_sites.c:82:16: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   82 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                ^~~
mask_sites.c:82:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   82 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                                                              ^~
mask_sites.c:107:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  107 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
mask_sites.c:107:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  107 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                    ^~
mask_sites.c:125:16: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  125 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                ^~~
mask_sites.c:125:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  125 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                                                              ^~
mask_sites.c:141:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  141 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
mask_sites.c:141:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  141 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                    ^~
mask_sites.c:150:16: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  150 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                ^~~
mask_sites.c:150:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  150 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                                                              ^~
mask_sites.c:34:50: warning: variable ‘cn’ set but not used [-Wunused-but-set-variable]
   34 |    int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
      |                                                  ^~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c mutation.c -o mutation.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c normalization.c -o normalization.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c output.c -o output.o
output.c: In function ‘print_bed’:
output.c:11:10: warning: unused variable ‘f1’ [-Wunused-variable]
   11 |    FILE *f1;
      |          ^~
output.c: In function ‘print_result_R’:
output.c:257:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  257 |          for (j=site[i].pos+pwmLen; j<min(site[i].pos+pwmLen+FLANKING_BASES,seqLen[site[i].seq]); j++)
      |          ^~~
output.c:260:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  260 |                         INTEGER(SeqIden)[increment_sequence]=site[i].seq+1;
      |                         ^~~~~~~
output.c:326:27: warning: unused variable ‘number’ [-Wunused-variable]
  326 |                       int number = id;
      |                           ^~~~~~
output.c:324:29: warning: unused variable ‘base’ [-Wunused-variable]
  324 |                  const char base[] = "m";
      |                             ^~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c pwm_score_distr.c -o pwm_score_distr.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c read_matrix.c -o read_matrix.o
read_matrix.c: In function ‘read_initial_pwm’:
read_matrix.c:22:8: warning: variable ‘checkfscanf’ set but not used [-Wunused-but-set-variable]
   22 |    int checkfscanf;
      |        ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c read_pwm0.c -o read_pwm0.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c read_seq.c -o read_seq.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c reverse_seq.c -o reverse_seq.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c scan_sites.c -o scan_sites.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c score_subsequence.c -o score_subsequence.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c selection.c -o selection.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c sort.c -o sort.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c top_kmers.c -o top_kmers.o
top_kmers.c: In function ‘count_k_tuples’:
top_kmers.c:332:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  332 |          for (k=0; k<kmerLen; k++)  s1[k]=seq[i][j+k];  s1[k]='\0';
      |          ^~~
top_kmers.c:332:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  332 |          for (k=0; k<kmerLen; k++)  s1[k]=seq[i][j+k];  s1[k]='\0';
      |                                                         ^~
top_kmers.c:333:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  333 |          for (k=0; k<kmerLen; k++)  s2[k]=rseq[i][seqLen[i]-kmerLen-j+k];  s2[k]='\0';
      |          ^~~
top_kmers.c:333:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  333 |          for (k=0; k<kmerLen; k++)  s2[k]=rseq[i][seqLen[i]-kmerLen-j+k];  s2[k]='\0';
      |                                                                            ^~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c transform_pwm.c -o transform_pwm.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c weights.c -o weights.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -fopenmp -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-rGADEM/00new/rGADEM/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rGADEM)