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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:rGADEM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings rGADEM_2.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/rGADEM.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rGADEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGADEM’ version ‘2.42.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rGADEM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’ ‘methods’ ‘seqLogo’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘GenomicRanges’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘rGADEM/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

GADEM: no visible global function definition for ‘seqlevels’
readGademPWMFile: no visible global function definition for ‘read.csv’
readPWMfile: no visible global function definition for ‘read.table’
readTransfacFile: no visible global function definition for
  ‘read.table’
[,gadem-ANY-ANY-ANY: no visible binding for global variable ‘ANY’
[,gadem-ANY-ANY-ANY : <anonymous>: no visible binding for global
  variable ‘gadem’
plot,gadem-ANY : <anonymous>: no visible global function definition for
  ‘makePWM’
plot,motif-ANY: no visible global function definition for ‘makePWM’
Undefined global functions or variables:
  ANY gadem makePWM read.csv read.table seqlevels
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
GADEM 62.889    0.1  33.096
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/rGADEM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rGADEM
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c alloc.c -o alloc.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c consensus.c -o consensus.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c crossover.c -o crossover.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c mutation.c -o mutation.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c normalization.c -o normalization.o
normalization.c: In function ‘range’:
normalization.c:124:13: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
  124 |   if(i==20) Rprintf("score is smaller than 10e-20\n");
      |             ^~~~~~~
      |             dprintf
gcc -I"/home/biocbuild/bbs-3.14-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:260:4: 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:326:13: warning: unused variable ‘number’ [-Wunused-variable]
  326 |         int number = id;
      |             ^~~~~~
output.c:324:15: warning: unused variable ‘base’ [-Wunused-variable]
  324 |    const char base[] = "m";
      |               ^~~~
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c selection.c -o selection.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c sort.c -o sort.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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)