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BioC 3.3: CHECK report for csaw on zin2

This page was generated on 2016-10-13 12:45:04 -0700 (Thu, 13 Oct 2016).

Package 261/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.6.1
Aaron Lun
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/csaw
Last Changed Rev: 117853 / Revision: 122332
Last Changed Date: 2016-05-25 11:12:49 -0700 (Wed, 25 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  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: 1.6.1
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings csaw_1.6.1.tar.gz
StartedAt: 2016-10-13 01:01:54 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:05:06 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 192.1 seconds
RetCode: 0
Status:  OK 
CheckDir: csaw.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings csaw_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/csaw.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.6.1’
* 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 ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
detailRanges 6.913  0.132   8.266
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
 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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c annotator.cpp -o annotator.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c bam_utils.cpp -o bam_utils.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c best_in_cluster.cpp -o best_in_cluster.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c get_cluster_stats.cpp -o get_cluster_stats.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c get_profile.cpp -o get_profile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c merge_windows.cpp -o merge_windows.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c pair_reads.cpp -o pair_reads.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c single_reads.cpp -o single_reads.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.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 pair_reads.o single_reads.o -L/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.3-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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
SEmethods0.2180.0000.218
checkBimodality0.2530.0040.257
clusterFDR1.0150.0001.018
clusterWindows2.1310.0002.131
combineTests0.0140.0040.017
consolidateClusters3.0780.0123.183
consolidateSizes0.490.000.49
correlateReads0.1080.0040.111
csawUsersGuide0.0010.0000.001
detailRanges6.9130.1328.266
extractReads0.9230.0000.936
filterWindows0.4620.0000.462
findMaxima0.0950.0000.095
getBestTest0.0110.0040.014
getPESizes0.0990.0040.104
getWidths0.4300.0000.445
maximizeCcf0.0020.0000.002
mergeWindows0.0350.0000.035
normOffsets0.9090.0000.932
overlapStats0.1320.0000.179
paramList0.1850.0070.195
profileSites0.4570.0080.467
readParam0.020.000.02
regionCounts0.2620.0000.262
scaledAverage0.3220.0000.323
strandedCounts1.2390.0041.242
upweightSummit0.0060.0000.006
windowCounts0.6680.0080.676
wwhm0.0680.0000.067