Package: edgeR

Version: 3.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.2.3.tar.gz

StartedAt: 2013-05-01 05:00:08 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:02:00 -0700 (Wed, 01 May 2013)

EllapsedTime: 112.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '3.2.3'
* 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 'edgeR' can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... 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 for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [13s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'edgeR-Tests.R' [9s/10s]
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 [9s/11s] OK
* 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

* installing *source* package 'edgeR' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_loess_by_col.cpp -o R_loess_by_col.o
R_loess_by_col.cpp:28:88: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i=0; i<ncols; ++i) { y_ptrs.push_back(i==0 ? NUMERIC_POINTER(y) : y_ptrs[i-1]+total); }
                                                                               ˜˜˜˜˜˜ ˜^˜
R_loess_by_col.cpp:36:108: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i=0; i<ncols; ++i) { f_ptrs.push_back(i==0 ? NUMERIC_POINTER(VECTOR_ELT(output, 0)) : f_ptrs[i-1]+total); }
                                                                                                   ˜˜˜˜˜˜ ˜^˜
R_loess_by_col.cpp:99:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]=0; }
                                              ˜˜˜˜˜˜ ^
R_loess_by_col.cpp:120:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]+=weight*y_ptrs[i][m]; }
                                              ˜˜˜˜˜˜ ^
R_loess_by_col.cpp:120:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]+=weight*y_ptrs[i][m]; }
                                                                       ˜˜˜˜˜˜ ^
R_loess_by_col.cpp:126:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]/=total_weight; }
                                              ˜˜˜˜˜˜ ^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_cr_adjust.cpp -o R_cr_adjust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_levenberg.cpp -o R_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_one_group.cpp -o R_one_group.o
R_one_group.cpp:24:27: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                ydptr=(double*) R_alloc(num_libs, sizeof(double));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_simple_good_turing.cpp -o R_simple_good_turing.o
R_simple_good_turing.cpp:25:35: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double* log_obs=(double*)R_alloc(rows, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c core/adj_coxreid.cpp -o core/adj_coxreid.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c core/glm_levenberg.cpp -o core/glm_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c core/glm_one_group.cpp -o core/glm_one_group.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c core/interpolator.cpp -o core/interpolator.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c core/fmm_spline.c -o core/fmm_spline.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)

name	user	system	elapsed
DGEList	0.041	0.005	0.055
WLEB	0.217	0.021	0.278
adjustedProfileLik	0.023	0.003	0.027
aveLogCPM	0.024	0.002	0.026
binomTest	0.013	0.001	0.013
calcNormFactors	0.020	0.001	0.020
camera.DGEList	0.284	0.012	0.305
commonCondLogLikDerDelta	0.014	0.001	0.085
condLogLikDerSize	0.073	0.000	0.074
cpm	0.010	0.001	0.010
cutWithMinN	0.008	0.000	0.009
dglmStdResid	0.092	0.005	0.226
dim	0.017	0.002	0.018
dispBinTrend	0.722	0.022	0.876
dispCoxReid	0.067	0.002	0.085
dispCoxReidInterpolateTagwise	0.080	0.004	0.094
dispCoxReidSplineTrend	1.267	0.014	1.513
edgeRUsersGuide	0.014	0.001	0.023
equalizeLibSizes	0.054	0.002	0.070
estimateCommonDisp	0.064	0.001	0.081
estimateDisp	0.452	0.006	0.554
estimateExonGenewisedisp	0.045	0.001	0.057
estimateGLMCommonDisp	0.144	0.004	0.173
estimateGLMTagwiseDisp	1.220	0.015	1.454
estimateGLMTrendedDisp	0.510	0.006	0.600
estimateTagwiseDisp	0.006	0.000	0.006
estimateTrendedDisp	1.321	0.027	1.640
exactTest	0.036	0.002	0.046
expandAsMatrix	0.013	0.001	0.016
getCounts	0.029	0.001	0.035
getPriorN	0.016	0.000	0.016
glmfit	0.124	0.003	0.159
gof	0.050	0.002	0.056
goodTuring	0.028	0.002	0.036
loessByCol	0.017	0.001	0.025
maPlot	0.034	0.002	0.039
maximizeInterpolant	0.011	0.002	0.014
maximizeQuadratic	0.011	0.001	0.012
meanvar	0.131	0.006	0.152
mglm	0.082	0.005	0.105
movingAverageByCol	0.010	0.001	0.010
plotBCV	1.025	0.022	1.222
plotExonUsage	0.023	0.002	0.029
plotMDS.DGEList	0.152	0.006	0.185
plotSmear	0.711	0.014	0.793
predFC	0.056	0.006	0.068
q2qnbinom	0.013	0.002	0.015
readDGE	0.008	0.000	0.010
roast.DGEList	0.320	0.008	0.404
spliceVariants	0.039	0.002	0.054
splitIntoGroups	0.015	0.001	0.018
subsetting	0.049	0.004	0.067
systematicSubset	0.009	0.001	0.011
thinCounts	0.007	0.001	0.009
topTags	0.058	0.004	0.068
weightedCondLogLikDerDelta	0.017	0.002	0.027
zscoreNBinom	0.006	0.001	0.007