rGADEM 1.0.1
Arnaud Droit
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/rGADEM | | Last Changed Rev: 48890 / Revision: 49923 | | Last Changed Date: 2010-08-19 09:15:51 -0700 (Thu, 19 Aug 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/rGADEM.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rGADEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rGADEM' version '1.0.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rGADEM' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'rGADEM' ...
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WARNING: this package has a configure script
It probably needs manual configuration
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** libs
making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:138: warning: unused variable 'nsitesEM'
Gadem_Analysis.c:159: warning: 'numTopWmerInB' may be used uninitialized in this function
Gadem_Analysis.c:132: warning: 'llrCutoff' may be used uninitialized in this function
Gadem_Analysis.c:126: warning: 'empDim' may be used uninitialized in this function
Gadem_Analysis.c:124: warning: 'llrDim' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c align_sites.c -o align_sites.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c alloc.c -o alloc.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c background.c -o background.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c base_frequency.c -o base_frequency.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c check_convergence.c -o check_convergence.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c check_pwm_dist.c -o check_pwm_dist.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c consensus.c -o consensus.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c construct_pwm.c -o construct_pwm.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c copy_pwm.c -o copy_pwm.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c crossover.c -o crossover.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c effect_seq_len.c -o effect_seq_len.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c evalue_meme.c -o evalue_meme.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c extend_alignment.c -o extend_alignment.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c initial_population.c -o initial_population.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c mask_sites.c -o mask_sites.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c mutation.c -o mutation.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c normalization.c -o normalization.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c output.c -o output.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c pwm_score_distr.c -o pwm_score_distr.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c read_matrix.c -o read_matrix.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c read_pwm0.c -o read_pwm0.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c read_seq.c -o read_seq.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c reverse_seq.c -o reverse_seq.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c scan_sites.c -o scan_sites.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c score_subsequence.c -o score_subsequence.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c selection.c -o selection.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c sort.c -o sort.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'top_kmer':
top_kmers.c:154: warning: 'numAvailableTopKmer' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c transform_pwm.c -o transform_pwm.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -IE:/biocbld/bbs-2.6-bioc/R/src/include -O3 -Wall -std=gnu99 -c weights.c -o weights.o
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 -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/rGADEM.Rcheck/rGADEM/libs
... done
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
Loading required package: GenomicRanges
Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rGADEM)