BioC 3.2: CHECK report for SGSeq on windows1.bioconductor.org
This page was generated on 2015-10-27 17:31:44 -0400 (Tue, 27 Oct 2015).
SGSeq 1.4.0 Leonard Goldstein
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/SGSeq | Last Changed Rev: 109589 / Revision: 109947 | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: SGSeq
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Version: 1.4.0
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Command: rm -rf SGSeq.buildbin-libdir SGSeq.Rcheck && mkdir SGSeq.buildbin-libdir SGSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SGSeq.buildbin-libdir SGSeq_1.4.0.tar.gz >SGSeq.Rcheck\00install.out 2>&1 && cp SGSeq.Rcheck\00install.out SGSeq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SGSeq.buildbin-libdir --install="check:SGSeq-install.out" --force-multiarch --no-vignettes --timings SGSeq_1.4.0.tar.gz
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StartedAt: 2015-10-27 05:34:35 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 05:43:17 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 522.2 seconds
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RetCode: 0
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Status: OK
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CheckDir: SGSeq.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf SGSeq.buildbin-libdir SGSeq.Rcheck && mkdir SGSeq.buildbin-libdir SGSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SGSeq.buildbin-libdir SGSeq_1.4.0.tar.gz >SGSeq.Rcheck\00install.out 2>&1 && cp SGSeq.Rcheck\00install.out SGSeq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SGSeq.buildbin-libdir --install="check:SGSeq-install.out" --force-multiarch --no-vignettes --timings SGSeq_1.4.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/SGSeq.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 'SGSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SGSeq' 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 'SGSeq' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'GenomicRanges:::extraColumnSlotNames'
'GenomicRanges:::extraColumnSlotsAsDF'
See the note in ?`:::` about the use of this operator.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeFeatures 13.50 0.20 13.70
predictVariantEffects 12.89 0.02 12.91
predictTxFeatures 6.80 0.06 6.86
** running examples for arch 'x64' ... [67s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeFeatures 16.31 0.29 16.59
predictVariantEffects 15.36 0.00 15.36
predictTxFeatures 7.94 0.08 8.01
getSGVariantCounts 7.13 0.09 7.22
getSGFeatureCounts 5.34 0.13 5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [74s]
[75s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [96s]
[97s] 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/SGSeq.Rcheck/00check.log'
for details.
SGSeq.Rcheck/00install.out:
install for i386
* installing *source* package 'SGSeq' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'SGSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SGSeq' as SGSeq_1.4.0.zip
* DONE (SGSeq)
SGSeq.Rcheck/examples_i386/SGSeq-Ex.timings:
name | user | system | elapsed
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SGFeatureCounts | 0.09 | 0.00 | 0.10 |
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SGFeatures | 0.03 | 0.00 | 0.03 |
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SGVariantCounts | 0.11 | 0.00 | 0.11 |
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SGVariants | 0.09 | 0.00 | 0.10 |
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TxFeatures | 0.07 | 0.00 | 0.06 |
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analyzeFeatures | 13.5 | 0.2 | 13.7 |
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analyzeVariants | 1.25 | 0.00 | 1.25 |
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annotate | 1.53 | 0.00 | 1.53 |
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assays | 0 | 0 | 0 |
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convertToSGFeatures | 1.92 | 0.02 | 1.94 |
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convertToTxFeatures | 0.48 | 0.00 | 0.48 |
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exportFeatures | 0 | 0 | 0 |
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findSGVariants | 1.1 | 0.0 | 1.1 |
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getBamInfo | 0.58 | 0.06 | 0.64 |
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getSGFeatureCounts | 3.98 | 0.07 | 4.04 |
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getSGVariantCounts | 4.94 | 0.04 | 4.99 |
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importTranscripts | 0 | 0 | 0 |
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makeSGFeatureCounts | 0.03 | 0.00 | 0.03 |
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makeVariantNames | 0 | 0 | 0 |
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mergeTxFeatures | 0.23 | 0.00 | 0.23 |
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plotCoverage | 0 | 0 | 0 |
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plotFeatures | 0 | 0 | 0 |
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plotSpliceGraph | 0 | 0 | 0 |
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plotVariants | 0 | 0 | 0 |
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predictTxFeatures | 6.80 | 0.06 | 6.86 |
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predictVariantEffects | 12.89 | 0.02 | 12.91 |
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processTerminalExons | 0.28 | 0.00 | 0.28 |
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slots | 0 | 0 | 0 |
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SGSeq.Rcheck/examples_x64/SGSeq-Ex.timings:
name | user | system | elapsed
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SGFeatureCounts | 0.12 | 0.00 | 0.12 |
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SGFeatures | 0.03 | 0.00 | 0.04 |
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SGVariantCounts | 0.16 | 0.00 | 0.16 |
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SGVariants | 0.11 | 0.00 | 0.11 |
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TxFeatures | 0.05 | 0.00 | 0.05 |
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analyzeFeatures | 16.31 | 0.29 | 16.59 |
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analyzeVariants | 1.46 | 0.00 | 1.46 |
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annotate | 1.37 | 0.00 | 1.37 |
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assays | 0 | 0 | 0 |
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convertToSGFeatures | 1.3 | 0.0 | 1.3 |
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convertToTxFeatures | 0.33 | 0.00 | 0.33 |
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exportFeatures | 0 | 0 | 0 |
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findSGVariants | 1.08 | 0.00 | 1.08 |
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getBamInfo | 0.72 | 0.12 | 0.84 |
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getSGFeatureCounts | 5.34 | 0.13 | 5.47 |
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getSGVariantCounts | 7.13 | 0.09 | 7.22 |
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importTranscripts | 0 | 0 | 0 |
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makeSGFeatureCounts | 0.04 | 0.00 | 0.05 |
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makeVariantNames | 0 | 0 | 0 |
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mergeTxFeatures | 0.3 | 0.0 | 0.3 |
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plotCoverage | 0 | 0 | 0 |
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plotFeatures | 0 | 0 | 0 |
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plotSpliceGraph | 0 | 0 | 0 |
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plotVariants | 0 | 0 | 0 |
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predictTxFeatures | 7.94 | 0.08 | 8.01 |
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predictVariantEffects | 15.36 | 0.00 | 15.36 |
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processTerminalExons | 0.33 | 0.00 | 0.32 |
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slots | 0 | 0 | 0 |
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