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Package 202/671HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 3.2.3
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/edgeR
Last Changed Rev: 75740 / Revision: 76155
Last Changed Date: 2013-04-17 01:55:00 -0700 (Wed, 17 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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

Command output

* 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

edgeR.Rcheck/00install.out:

* 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)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.0410.0050.055
WLEB0.2170.0210.278
adjustedProfileLik0.0230.0030.027
aveLogCPM0.0240.0020.026
binomTest0.0130.0010.013
calcNormFactors0.0200.0010.020
camera.DGEList0.2840.0120.305
commonCondLogLikDerDelta0.0140.0010.085
condLogLikDerSize0.0730.0000.074
cpm0.0100.0010.010
cutWithMinN0.0080.0000.009
dglmStdResid0.0920.0050.226
dim0.0170.0020.018
dispBinTrend0.7220.0220.876
dispCoxReid0.0670.0020.085
dispCoxReidInterpolateTagwise0.0800.0040.094
dispCoxReidSplineTrend1.2670.0141.513
edgeRUsersGuide0.0140.0010.023
equalizeLibSizes0.0540.0020.070
estimateCommonDisp0.0640.0010.081
estimateDisp0.4520.0060.554
estimateExonGenewisedisp0.0450.0010.057
estimateGLMCommonDisp0.1440.0040.173
estimateGLMTagwiseDisp1.2200.0151.454
estimateGLMTrendedDisp0.5100.0060.600
estimateTagwiseDisp0.0060.0000.006
estimateTrendedDisp1.3210.0271.640
exactTest0.0360.0020.046
expandAsMatrix0.0130.0010.016
getCounts0.0290.0010.035
getPriorN0.0160.0000.016
glmfit0.1240.0030.159
gof0.0500.0020.056
goodTuring0.0280.0020.036
loessByCol0.0170.0010.025
maPlot0.0340.0020.039
maximizeInterpolant0.0110.0020.014
maximizeQuadratic0.0110.0010.012
meanvar0.1310.0060.152
mglm0.0820.0050.105
movingAverageByCol0.0100.0010.010
plotBCV1.0250.0221.222
plotExonUsage0.0230.0020.029
plotMDS.DGEList0.1520.0060.185
plotSmear0.7110.0140.793
predFC0.0560.0060.068
q2qnbinom0.0130.0020.015
readDGE0.0080.0000.010
roast.DGEList0.3200.0080.404
spliceVariants0.0390.0020.054
splitIntoGroups0.0150.0010.018
subsetting0.0490.0040.067
systematicSubset0.0090.0010.011
thinCounts0.0070.0010.009
topTags0.0580.0040.068
weightedCondLogLikDerDelta0.0170.0020.027
zscoreNBinom0.0060.0010.007