Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for csaw on linux1.bioconductor.org

This page was generated on 2015-10-27 17:26:49 -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: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings csaw_1.4.0.tar.gz
StartedAt: 2015-10-27 02:38:48 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:42:18 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 210.3 seconds
RetCode: 0
Status:  OK 
CheckDir: csaw.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings csaw_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/csaw.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘csaw’ can be installed ... [22s/22s] 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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
detailRanges 8.716   0.04   8.756
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’ [16s/16s]
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
 [16s/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: OK

csaw.Rcheck/00install.out:

* installing *source* package ‘csaw’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c annotator.cpp -o annotator.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c best_in_cluster.cpp -o best_in_cluster.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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 [-Wmaybe-uninitialized]
    while (right_copy >= is_max) { 
    ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c get_cluster_stats.cpp -o get_cluster_stats.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c get_profile.cpp -o get_profile.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c merge_windows.cpp -o merge_windows.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o csaw.so 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 -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/csaw.Rcheck/csaw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (csaw)

csaw.Rcheck/csaw-Ex.timings:

nameusersystemelapsed
SEmethods0.4670.0040.471
checkBimodality1.0580.0081.066
clusterFDR0.0370.0000.037
combineTests0.0240.0040.028
consolidateSizes1.1990.0001.199
correlateReads0.3320.0000.332
csawUsersGuide0.0010.0000.001
detailRanges8.7160.0408.756
dumpPE0.9520.0320.984
extractReads1.2110.0041.216
filterWindows1.0590.0001.058
findMaxima0.2550.0000.256
getBestTest0.020.000.02
getPESizes0.290.000.29
getWidths1.2010.0001.200
makeExtVector0.0020.0000.001
maximizeCcf0.0020.0000.003
mergeWindows0.0550.0000.054
normOffsets1.1670.0041.171
overlapStats0.3200.0040.325
paramList0.4990.0000.499
profileSites1.2930.0001.292
readParam0.0220.0000.023
regionCounts0.8090.0000.808
scaledAverage0.5420.0000.542
strandedCounts2.7840.0042.789
upweightSummit0.0050.0000.004
windowCounts1.3550.0041.359
wwhm0.1070.0000.107