rGADEM 2.6.0
Arnaud Droit
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/rGADEM | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/rGADEM.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-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 ‘2.6.0’
* 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 whether package ‘rGADEM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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.
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/rGADEM.Rcheck/rGADEM/libs/rGADEM.so’:
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘Gadem_Analysis.o’, ‘alloc.o’, ‘background.o’,
‘evalue_meme.o’, ‘output.o’, ‘pwm_score_distr.o’,
‘read_matrix.o’, ‘read_seq.o’, ‘scan_sites.o’, ‘selection.o’
Found ‘printf’, possibly from ‘printf’ (C)
Objects: ‘Gadem_Analysis.o’, ‘background.o’, ‘output.o’,
‘read_matrix.o’, ‘scan_sites.o’, ‘top_kmers.o’
Found ‘putchar’, possibly from ‘putchar’ (C)
Object: ‘Gadem_Analysis.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘Gadem_Analysis.o’, ‘alloc.o’, ‘background.o’,
‘evalue_meme.o’, ‘normalization.o’, ‘output.o’,
‘pwm_score_distr.o’, ‘read_matrix.o’, ‘read_seq.o’,
‘scan_sites.o’, ‘selection.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘evalue_meme.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GADEM 86.645 4.848 49.109
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/rGADEM.Rcheck/00check.log’
for details.
* installing *source* package ‘rGADEM’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc -std=gnu99 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
config.status: src/config.h is unchanged
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:182:59: warning: variable ‘totalSitesInput’ set but not used [-Wunused-but-set-variable]
Gadem_Analysis.c:174:7: warning: variable ‘generationNoMotif’ set but not used [-Wunused-but-set-variable]
Gadem_Analysis.c:113:12: warning: variable ‘logepwm’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c align_sites.c -o align_sites.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c alloc.c -o alloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c background.c -o background.o
background.c: In function ‘ll_score_backg_model’:
background.c:1094:10: warning: variable ‘s1’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c base_frequency.c -o base_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c check_convergence.c -o check_convergence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c check_pwm_dist.c -o check_pwm_dist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c consensus.c -o consensus.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c construct_pwm.c -o construct_pwm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c copy_pwm.c -o copy_pwm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c crossover.c -o crossover.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c effect_seq_len.c -o effect_seq_len.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c evalue_meme.c -o evalue_meme.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c extend_alignment.c -o extend_alignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c initial_population.c -o initial_population.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:34:50: warning: variable ‘cn’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c mutation.c -o mutation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c normalization.c -o normalization.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c output.c -o output.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c pwm_score_distr.c -o pwm_score_distr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:21:8: warning: variable ‘checkfscanf’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_pwm0.c -o read_pwm0.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_seq.c -o read_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c reverse_seq.c -o reverse_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c scan_sites.c -o scan_sites.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c score_subsequence.c -o score_subsequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c selection.c -o selection.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sort.c -o sort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c top_kmers.c -o top_kmers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c transform_pwm.c -o transform_pwm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c weights.c -o weights.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/rGADEM.Rcheck/rGADEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘rGADEM.Rnw’
** testing if installed package can be loaded
* DONE (rGADEM)