Patrick C.N. Martin
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ChIPanalyser |
| Branch: RELEASE_3_8 |
| Last Commit: b5a2283 |
| Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:14 -0400 (Sat, 13 Apr 2019).
| Package 242/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPanalyser 1.4.0 Patrick C.N. Martin
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ChIPanalyser |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPanalyser.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ChIPanalyser_1.4.0.tar.gz |
| StartedAt: 2019-04-13 01:08:40 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:14:50 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 370.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChIPanalyser.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPanalyser.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ChIPanalyser_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ChIPanalyser.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPanalyser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPanalyser' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'ChIPanalyser' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency.Rd:32: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency.Rd:34: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency_-.Rd:41: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency_-.Rd:59: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency_-.Rd:60: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/NoAccess.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeChipProfile.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeChipProfile.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeChipProfile.Rd:92: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:20: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:23: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOccupancy.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOccupancy.Rd:74: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:24: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:87: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:20: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/data.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/data.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/data.Rd:33: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/genomicProfileParameters-class.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/genomicProfileParameters.Rd:63: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:27: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/processingChIPseq.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/processingChIPseq.Rd:30: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/processingChIPseq.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/profileAccuracyEstimate.Rd:27: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/profileAccuracyEstimate.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ChIPanalyser.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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomicProfileParameters-class 6.29 0.28 6.58
genomicProfileParameters 5.41 0.28 5.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomicProfileParameters-class 6.07 0.22 6.28
* 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-3.8-bioc/meat/ChIPanalyser.Rcheck/00check.log'
for details.
ChIPanalyser.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ChIPanalyser_1.4.0.tar.gz && rm -rf ChIPanalyser.buildbin-libdir && mkdir ChIPanalyser.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPanalyser.buildbin-libdir ChIPanalyser_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser_1.4.0.zip && rm ChIPanalyser_1.4.0.tar.gz ChIPanalyser_1.4.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 553k 100 553k 0 0 12.3M 0 --:--:-- --:--:-- --:--:-- 13.5M
install for i386
* installing *source* package 'ChIPanalyser' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ChIPanalyser'
finding HTML links ... done
AllSitesAboveThreshold html
finding level-2 HTML links ... done
BPFrequency html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency.Rd:32: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency.Rd:34: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
BPFrequency_- html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency_-.Rd:41: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency_-.Rd:59: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/BPFrequency_-.Rd:60: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
ChIPanalyser-package html
DNASequenceLength html
DNASequenceLength_- html
GRList-class html
NoAccess html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/NoAccess.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
PFMFormat html
PFMFormat_ html
PWMThreshold html
PWMThreshold_- html
PWMpseudocount html
PWMpseudocount_- html
PositionFrequencyMatrix html
PositionFrequencyMatrix_- html
PositionWeightMatrix html
PositionWeightMatrix_- html
ScalingFactorPWM html
ScalingFactorPWM_- html
averageExpPWMScore html
backgroundSignal html
backgroundSignal_- html
boundMolecules html
boundMolecules_- html
chipMean html
chipMean_- html
chipSd html
chipSd_- html
chipSmooth html
chipSmooth_- html
computeChipProfile html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeChipProfile.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeChipProfile.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeChipProfile.Rd:92: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
computeGenomeWidePWMScore html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:20: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:23: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
computeOccupancy html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOccupancy.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOccupancy.Rd:74: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
computeOptimal html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:24: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computeOptimal.Rd:87: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
computePWMScore html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:20: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/computePWMScore.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
data html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/data.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/data.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/data.Rd:33: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
genomicProfileParameters-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/genomicProfileParameters-class.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
genomicProfileParameters html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/genomicProfileParameters.Rd:63: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
maxPWMScore html
maxSignal html
maxSignal_- html
minPWMScore html
naturalLog html
naturalLog_- html
noOfSites html
noOfSites_- html
occupancyProfileParameters-class html
occupancyProfileParameters html
ploidy html
ploidy_- html
plotOccupancyProfile html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:27: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/plotOccupancyProfile.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
plotOptimalHeatMaps html
processingChIPseq html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/processingChIPseq.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/processingChIPseq.Rd:30: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/processingChIPseq.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
profileAccuracyEstimate html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/profileAccuracyEstimate.Rd:27: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpuo7TQb/R.INSTALL233c1de42930/ChIPanalyser/man/profileAccuracyEstimate.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
removeBackground html
removeBackground_- html
searchSites html
stepSize html
stepSize_- html
strandRule html
strandRule_- html
whichstrand html
whichstrand_- html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ChIPanalyser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPanalyser' as ChIPanalyser_1.4.0.zip
* DONE (ChIPanalyser)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ChIPanalyser' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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ChIPanalyser.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("ChIPanalyser")
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BSgenome.Dmelanogaster.UCSC.dm3
RUNIT TEST PROTOCOL -- Sat Apr 13 01:14:24 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChIPanalyser RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
14.65 0.82 15.50
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ChIPanalyser.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("ChIPanalyser")
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BSgenome.Dmelanogaster.UCSC.dm3
RUNIT TEST PROTOCOL -- Sat Apr 13 01:14:39 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChIPanalyser RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
14.03 0.50 14.53
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ChIPanalyser.Rcheck/examples_i386/ChIPanalyser-Ex.timings
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ChIPanalyser.Rcheck/examples_x64/ChIPanalyser-Ex.timings
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