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BioC 3.2: CHECK report for csaw on windows1.bioconductor.org

This page was generated on 2015-10-27 17:31:43 -0400 (Tue, 27 Oct 2015).

Package 239/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.4.0
Aaron Lun
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/csaw
Last Changed Rev: 109614 / Revision: 109947
Last Changed Date: 2015-10-14 12:14:32 -0400 (Wed, 14 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: csaw
Version: 1.4.0
Command: rm -rf csaw.buildbin-libdir csaw.Rcheck && mkdir csaw.buildbin-libdir csaw.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=csaw.buildbin-libdir csaw_1.4.0.tar.gz >csaw.Rcheck\00install.out 2>&1 && cp csaw.Rcheck\00install.out csaw-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=csaw.buildbin-libdir --install="check:csaw-install.out" --force-multiarch --no-vignettes --timings csaw_1.4.0.tar.gz
StartedAt: 2015-10-27 01:01:14 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:06:20 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 305.7 seconds
RetCode: 0
Status:  OK  
CheckDir: csaw.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf csaw.buildbin-libdir csaw.Rcheck && mkdir csaw.buildbin-libdir csaw.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=csaw.buildbin-libdir csaw_1.4.0.tar.gz >csaw.Rcheck\00install.out 2>&1 && cp csaw.Rcheck\00install.out csaw-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=csaw.buildbin-libdir --install="check:csaw-install.out" --force-multiarch --no-vignettes --timings csaw_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/csaw.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'csaw/DESCRIPTION' ... OK
* this is package 'csaw' version '1.4.0'
* 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 'csaw' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 ... 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 line endings in C/C++/Fortran sources/headers ... 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:/biocbld/bbs-3.2-bioc/meat/csaw.buildbin-libdir/csaw/libs/i386/csaw.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/csaw.buildbin-libdir/csaw/libs/x64/csaw.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
detailRanges 7.52    0.3    7.85
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
detailRanges 8.64   0.26    8.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-basic.R' [14s]
  Comparing 'test-basic.Rout' to 'test-basic.Rout.save' ... OK
 [14s] OK
** running tests for arch 'x64' ...
  Running 'test-basic.R' [16s]
  Comparing 'test-basic.Rout' to 'test-basic.Rout.save' ... OK
 [16s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/csaw.Rcheck/00check.log'
for details.


csaw.Rcheck/00install.out:


install for i386

* installing *source* package 'csaw' ...
** libs
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c annotator.cpp -o annotator.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c best_in_cluster.cpp -o best_in_cluster.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c check_bimodality.cpp -o check_bimodality.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c correlate_reads.cpp -o correlate_reads.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c find_maxima.cpp -o find_maxima.o
find_maxima.cpp: In function 'SEXPREC* find_maxima(SEXP, SEXP, SEXP, SEXP, SEXP)':
find_maxima.cpp:90:4: warning: 'is_max' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c get_cluster_stats.cpp -o get_cluster_stats.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c get_profile.cpp -o get_profile.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c get_rle_counts.cpp -o get_rle_counts.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c merge_windows.cpp -o merge_windows.o
g++ -m32 -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/csaw.buildbin-libdir/csaw/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'csaw' ...
** libs
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c annotator.cpp -o annotator.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c best_in_cluster.cpp -o best_in_cluster.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c check_bimodality.cpp -o check_bimodality.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c correlate_reads.cpp -o correlate_reads.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c find_maxima.cpp -o find_maxima.o
find_maxima.cpp: In function 'SEXPREC* find_maxima(SEXP, SEXP, SEXP, SEXP, SEXP)':
find_maxima.cpp:90:4: warning: 'is_max' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c get_cluster_stats.cpp -o get_cluster_stats.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c get_profile.cpp -o get_profile.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c get_rle_counts.cpp -o get_rle_counts.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c merge_windows.cpp -o merge_windows.o
g++ -m64 -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/csaw.buildbin-libdir/csaw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'csaw' as csaw_1.4.0.zip
* DONE (csaw)

csaw.Rcheck/examples_i386/csaw-Ex.timings:

nameusersystemelapsed
SEmethods0.280.000.28
checkBimodality0.660.020.67
clusterFDR0.010.000.02
combineTests0.020.000.02
consolidateSizes0.700.020.71
correlateReads0.420.000.43
csawUsersGuide000
detailRanges7.520.307.85
dumpPE0.610.050.65
extractReads0.760.010.78
filterWindows0.710.000.71
findMaxima0.150.000.15
getBestTest0.020.000.02
getPESizes0.200.020.22
getWidths0.840.000.85
makeExtVector000
maximizeCcf000
mergeWindows0.030.000.03
normOffsets0.740.080.82
overlapStats0.170.020.19
paramList0.320.010.33
profileSites0.810.020.83
readParam0.010.000.01
regionCounts0.470.000.47
scaledAverage0.500.010.52
strandedCounts1.920.071.98
upweightSummit000
windowCounts1.220.011.23
wwhm0.050.000.05

csaw.Rcheck/examples_x64/csaw-Ex.timings:

nameusersystemelapsed
SEmethods0.320.000.33
checkBimodality0.710.010.72
clusterFDR0.030.000.03
combineTests0.010.000.01
consolidateSizes0.990.000.99
correlateReads0.360.000.36
csawUsersGuide000
detailRanges8.640.268.91
dumpPE0.890.020.92
extractReads1.410.001.41
filterWindows0.890.000.89
findMaxima0.180.000.19
getBestTest0.020.000.01
getPESizes0.200.010.22
getWidths1.240.041.27
makeExtVector000
maximizeCcf0.010.000.01
mergeWindows0.060.000.06
normOffsets1.160.041.21
overlapStats0.220.000.22
paramList0.390.020.40
profileSites1.030.011.05
readParam0.030.000.03
regionCounts0.960.000.95
scaledAverage0.750.000.75
strandedCounts2.540.032.58
upweightSummit000
windowCounts1.250.021.26
wwhm0.080.000.08