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).
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 ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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
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###
### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings csaw_1.4.0.tar.gz
###
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* 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:
| name | user | system | elapsed
|
| SEmethods | 0.467 | 0.004 | 0.471 |
|
| checkBimodality | 1.058 | 0.008 | 1.066 |
|
| clusterFDR | 0.037 | 0.000 | 0.037 |
|
| combineTests | 0.024 | 0.004 | 0.028 |
|
| consolidateSizes | 1.199 | 0.000 | 1.199 |
|
| correlateReads | 0.332 | 0.000 | 0.332 |
|
| csawUsersGuide | 0.001 | 0.000 | 0.001 |
|
| detailRanges | 8.716 | 0.040 | 8.756 |
|
| dumpPE | 0.952 | 0.032 | 0.984 |
|
| extractReads | 1.211 | 0.004 | 1.216 |
|
| filterWindows | 1.059 | 0.000 | 1.058 |
|
| findMaxima | 0.255 | 0.000 | 0.256 |
|
| getBestTest | 0.02 | 0.00 | 0.02 |
|
| getPESizes | 0.29 | 0.00 | 0.29 |
|
| getWidths | 1.201 | 0.000 | 1.200 |
|
| makeExtVector | 0.002 | 0.000 | 0.001 |
|
| maximizeCcf | 0.002 | 0.000 | 0.003 |
|
| mergeWindows | 0.055 | 0.000 | 0.054 |
|
| normOffsets | 1.167 | 0.004 | 1.171 |
|
| overlapStats | 0.320 | 0.004 | 0.325 |
|
| paramList | 0.499 | 0.000 | 0.499 |
|
| profileSites | 1.293 | 0.000 | 1.292 |
|
| readParam | 0.022 | 0.000 | 0.023 |
|
| regionCounts | 0.809 | 0.000 | 0.808 |
|
| scaledAverage | 0.542 | 0.000 | 0.542 |
|
| strandedCounts | 2.784 | 0.004 | 2.789 |
|
| upweightSummit | 0.005 | 0.000 | 0.004 |
|
| windowCounts | 1.355 | 0.004 | 1.359 |
|
| wwhm | 0.107 | 0.000 | 0.107 |
|