Arnaud Droit
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/rGADEM |
| Branch: RELEASE_3_7 |
| Last Commit: 4d2b90a |
| Last Changed Date: 2018-04-30 10:35:12 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:34:35 -0400 (Wed, 17 Oct 2018).
| Package 1227/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rGADEM 2.28.0 Arnaud Droit
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rGADEM |
| Version: 2.28.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rGADEM_2.28.0.tar.gz |
| StartedAt: 2018-10-17 04:22:42 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:30:11 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 449.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rGADEM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rGADEM_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rGADEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rGADEM' version '2.28.0'
* 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 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' 'IRanges' '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
* 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'.
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
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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/rGADEM/libs/i386/rGADEM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GADEM 100.64 3.54 104.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GADEM 91.26 0.47 91.77
* 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.Rcheck/00check.log'
for details.
rGADEM.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rGADEM_2.28.0.tar.gz && rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rGADEM.buildbin-libdir rGADEM_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rGADEM_2.28.0.zip && rm rGADEM_2.28.0.tar.gz rGADEM_2.28.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 121k 100 121k 0 0 2089k 0 --:--:-- --:--:-- --:--:-- 2341k
install for i386
* installing *source* package 'rGADEM' ...
configure.win...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable]
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]
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]
double **logepwm; // log(em-optimized PWM)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c align_sites.c -o align_sites.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c alloc.c -o alloc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c background.c -o background.o
background.c: In function 'll_score_backg_model':
background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
char *s1;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c base_frequency.c -o base_frequency.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c check_convergence.c -o check_convergence.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c check_pwm_dist.c -o check_pwm_dist.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c consensus.c -o consensus.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c construct_pwm.c -o construct_pwm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c copy_pwm.c -o copy_pwm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c crossover.c -o crossover.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c effect_seq_len.c -o effect_seq_len.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c evalue_meme.c -o evalue_meme.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c extend_alignment.c -o extend_alignment.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c initial_population.c -o initial_population.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mask_sites.c -o mask_sites.o
mask_sites.c: In function 'mask_repetitive':
mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable]
int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mutation.c -o mutation.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c normalization.c -o normalization.o
normalization.c: In function 'range':
normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
if(i==20) Rprintf("score is smaller than 10e-20\n");
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c output.c -o output.o
output.c: In function 'print_bed':
output.c:11:10: warning: unused variable 'f1' [-Wunused-variable]
FILE *f1;
^
output.c: In function 'print_result_R':
output.c:326:13: warning: unused variable 'number' [-Wunused-variable]
int number = id;
^
output.c:324:15: warning: unused variable 'base' [-Wunused-variable]
const char base[] = "m";
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c pwm_score_distr.c -o pwm_score_distr.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int checkfscanf;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_pwm0.c -o read_pwm0.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_seq.c -o read_seq.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c reverse_seq.c -o reverse_seq.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sample_wo_replacement.c -o sample_wo_replacement.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c scan_sites.c -o scan_sites.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c score_subsequence.c -o score_subsequence.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c selection.c -o selection.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sort.c -o sort.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c top_kmers.c -o top_kmers.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c transform_pwm.c -o transform_pwm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c weights.c -o weights.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rGADEM.dll tmp.def 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 -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rGADEM'
finding HTML links ... done
GADEM html
align-class html
gadem-class html
motif-class html
parameters-class html
readPWMfile html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'rGADEM' ...
configure.win...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable]
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]
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]
double **logepwm; // log(em-optimized PWM)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c align_sites.c -o align_sites.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c alloc.c -o alloc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c background.c -o background.o
background.c: In function 'll_score_backg_model':
background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
char *s1;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c base_frequency.c -o base_frequency.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c check_convergence.c -o check_convergence.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c check_pwm_dist.c -o check_pwm_dist.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c consensus.c -o consensus.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c construct_pwm.c -o construct_pwm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c copy_pwm.c -o copy_pwm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c crossover.c -o crossover.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c effect_seq_len.c -o effect_seq_len.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c evalue_meme.c -o evalue_meme.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extend_alignment.c -o extend_alignment.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c initial_population.c -o initial_population.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mask_sites.c -o mask_sites.o
mask_sites.c: In function 'mask_repetitive':
mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable]
int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mutation.c -o mutation.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c normalization.c -o normalization.o
normalization.c: In function 'range':
normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
if(i==20) Rprintf("score is smaller than 10e-20\n");
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c output.c -o output.o
output.c: In function 'print_bed':
output.c:11:10: warning: unused variable 'f1' [-Wunused-variable]
FILE *f1;
^
output.c: In function 'print_result_R':
output.c:326:13: warning: unused variable 'number' [-Wunused-variable]
int number = id;
^
output.c:324:15: warning: unused variable 'base' [-Wunused-variable]
const char base[] = "m";
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c pwm_score_distr.c -o pwm_score_distr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int checkfscanf;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_pwm0.c -o read_pwm0.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_seq.c -o read_seq.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c reverse_seq.c -o reverse_seq.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sample_wo_replacement.c -o sample_wo_replacement.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c scan_sites.c -o scan_sites.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c score_subsequence.c -o score_subsequence.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c selection.c -o selection.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sort.c -o sort.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c top_kmers.c -o top_kmers.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c transform_pwm.c -o transform_pwm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c weights.c -o weights.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rGADEM.dll tmp.def 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 -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_2.28.0.zip
* DONE (rGADEM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'rGADEM' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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rGADEM.Rcheck/examples_i386/rGADEM-Ex.timings
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rGADEM.Rcheck/examples_x64/rGADEM-Ex.timings
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