Jianhong Ou
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/InPAS |
| Branch: RELEASE_3_6 |
| Last Commit: 80e858d |
| Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:25:56 -0400 (Thu, 12 Apr 2018).
| Package 696/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| InPAS 1.10.0 Jianhong Ou
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: InPAS |
| Version: 1.10.0 |
| Command: rm -rf InPAS.buildbin-libdir InPAS.Rcheck && mkdir InPAS.buildbin-libdir InPAS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InPAS.buildbin-libdir InPAS_1.10.0.tar.gz >InPAS.Rcheck\00install.out 2>&1 && cp InPAS.Rcheck\00install.out InPAS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=InPAS.buildbin-libdir --install="check:InPAS-install.out" --force-multiarch --no-vignettes --timings InPAS_1.10.0.tar.gz |
| StartedAt: 2018-04-12 00:50:25 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:58:46 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 501.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InPAS.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf InPAS.buildbin-libdir InPAS.Rcheck && mkdir InPAS.buildbin-libdir InPAS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InPAS.buildbin-libdir InPAS_1.10.0.tar.gz >InPAS.Rcheck\00install.out 2>&1 && cp InPAS.Rcheck\00install.out InPAS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=InPAS.buildbin-libdir --install="check:InPAS-install.out" --force-multiarch --no-vignettes --timings InPAS_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InPAS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InPAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'InPAS' version '1.10.0'
* 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 'InPAS' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsite_estimation.Rd:73: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:26: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:37: missing file link 'cleanUpdTSeq'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:45: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:48: missing file link 'PASclassifier'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:58: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/PAscore.Rd:30: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/PAscore2.Rd:30: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3eSet.Rd:20: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3eSet.Rd:38: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3eSet.Rd:39: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3usage.Rd:25: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/covThreshold.Rd:19: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/covThreshold.Rd:22: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/coverageFromBedGraph.Rd:21: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/coverageRate.Rd:20: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/coverageRate.Rd:41: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/distalAdj.Rd:27: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/getCov.Rd:17: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/getUTR3eSet.Rd:25: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/getUTR3eSet.Rd:37: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:43: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:45: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:72: missing file link 'cleanUpdTSeq'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:75: missing file link 'PASclassifier'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:116: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/lastCDSusage.Rd:23: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/proximalAdj.Rd:25: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/proximalAdjByCleanUpdTSeq.Rd:32: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/proximalAdjByPWM.Rd:32: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/seqLen.Rd:14: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/seqLen.Rd:24: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/testUsage.Rd:22: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/testUsage.Rd:25: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/totalCoverage.Rd:18: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/usage4plot.Rd:17: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3Annotation.Rd:4: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3Annotation.Rd:7: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3Annotation.Rd:15: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3UsageEstimation.Rd:23: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3UsageEstimation.Rd:36: missing file link 'BiocParallelParam'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InPAS.Rcheck/00install.out' for details.
* 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 ... 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 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
filterRes 7.24 0.22 7.45
getUTR3eSet 6.12 0.03 6.16
testUsage 5.73 0.01 5.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
filterRes 7.61 0.13 7.73
getUTR3eSet 6.56 0.00 6.56
testUsage 5.91 0.05 5.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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 WARNING
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/InPAS.Rcheck/00check.log'
for details.
InPAS.Rcheck/00install.out
install for i386
* installing *source* package 'InPAS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'InPAS'
finding HTML links ... done
CPsite_estimation html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsite_estimation.Rd:73: missing file link 'BSgenome'
CPsites html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:26: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:37: missing file link 'cleanUpdTSeq'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:45: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:48: missing file link 'PASclassifier'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/CPsites.Rd:58: missing file link 'BiocParallelParam'
InPAS-package html
PAscore html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/PAscore.Rd:30: missing file link 'BSgenome'
PAscore2 html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/PAscore2.Rd:30: missing file link 'BSgenome'
UTR3TotalCoverage html
UTR3eSet html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3eSet.Rd:20: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3eSet.Rd:38: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3eSet.Rd:39: missing file link 'GRanges'
UTR3usage html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/UTR3usage.Rd:25: missing file link 'BiocParallelParam'
covThreshold html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/covThreshold.Rd:19: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/covThreshold.Rd:22: missing file link 'TxDb'
coverageFromBedGraph html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/coverageFromBedGraph.Rd:21: missing file link 'BiocParallelParam'
coverageRate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/coverageRate.Rd:20: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/coverageRate.Rd:41: missing file link 'GRanges'
depthWeight html
distalAdj html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/distalAdj.Rd:27: missing file link 'BSgenome'
filterRes html
fisher.exact.test html
get.regions.coverage html
getCov html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/getCov.Rd:17: missing file link 'BSgenome'
getUTR3eSet html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/getUTR3eSet.Rd:25: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/getUTR3eSet.Rd:37: missing file link 'BiocParallelParam'
getUTR3region html
inPAS html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:43: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:45: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:72: missing file link 'cleanUpdTSeq'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:75: missing file link 'PASclassifier'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/inPAS.Rd:116: missing file link 'BiocParallelParam'
lastCDSusage html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/lastCDSusage.Rd:23: missing file link 'BiocParallelParam'
limmaAnalyze html
optimalSegmentation html
polishCPs html
prepare4GSEA html
proximalAdj html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/proximalAdj.Rd:25: missing file link 'BSgenome'
proximalAdjByCleanUpdTSeq html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/proximalAdjByCleanUpdTSeq.Rd:32: missing file link 'BSgenome'
proximalAdjByPWM html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/proximalAdjByPWM.Rd:32: missing file link 'BSgenome'
removeUTR3__UTR3 html
searchDistalCPs html
searchProximalCPs html
seqLen html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/seqLen.Rd:14: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/seqLen.Rd:24: missing file link 'seqlengths'
singleGroupAnalyze html
singleSampleAnalyze html
finding level-2 HTML links ... done
sortGR html
testUsage html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/testUsage.Rd:22: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/testUsage.Rd:25: missing file link 'BiocParallelParam'
totalCoverage html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/totalCoverage.Rd:18: missing file link 'BSgenome'
trimSeqnames html
usage4plot html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/usage4plot.Rd:17: missing file link 'BSgenome'
utr3.hg19 html
utr3.mm10 html
utr3Annotation html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3Annotation.Rd:4: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3Annotation.Rd:7: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3Annotation.Rd:15: missing file link 'TxDb'
utr3UsageEstimation html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3UsageEstimation.Rd:23: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsVWdP4/R.INSTALL2d2c1a53f62/InPAS/man/utr3UsageEstimation.Rd:36: missing file link 'BiocParallelParam'
valley html
zScoreThrethold html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'InPAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InPAS' as InPAS_1.10.0.zip
* DONE (InPAS)
In R CMD INSTALL
In R CMD INSTALL
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InPAS.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("BSgenome.Mmusculus.UCSC.mm10") || stop("can not load BSgenome.")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("can not load BSgenome.")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load TxDb")
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> require("rtracklayer") || stop("can not load rtracklayer.")
[1] TRUE
> require("limma") || stop("can not load limma")
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
[1] TRUE
> BiocGenerics:::testPackage("InPAS")
seqlevelsStyle of genome is different from bedgraph file.
RUNIT TEST PROTOCOL -- Thu Apr 12 00:58:12 2018
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
InPAS RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
21.01 0.75 21.90
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InPAS.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("BSgenome.Mmusculus.UCSC.mm10") || stop("can not load BSgenome.")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("can not load BSgenome.")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load TxDb")
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> require("rtracklayer") || stop("can not load rtracklayer.")
[1] TRUE
> require("limma") || stop("can not load limma")
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
[1] TRUE
> BiocGenerics:::testPackage("InPAS")
seqlevelsStyle of genome is different from bedgraph file.
RUNIT TEST PROTOCOL -- Thu Apr 12 00:58:39 2018
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
InPAS RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
26.01 0.62 26.79
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InPAS.Rcheck/examples_i386/InPAS-Ex.timings
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InPAS.Rcheck/examples_x64/InPAS-Ex.timings
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