Lihua Julie Zhu
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GUIDEseq |
| Branch: RELEASE_3_8 |
| Last Commit: e6c1cdf |
| Last Changed Date: 2019-01-04 13:35:20 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:01 -0400 (Sat, 13 Apr 2019).
| Package 699/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GUIDEseq 1.12.1 Lihua Julie Zhu
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GUIDEseq |
| Version: 1.12.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GUIDEseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GUIDEseq_1.12.1.tar.gz |
| StartedAt: 2019-04-13 02:57:02 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:03:35 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 392.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GUIDEseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GUIDEseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GUIDEseq_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GUIDEseq.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 'GUIDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GUIDEseq' version '1.12.1'
* 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 'GUIDEseq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
extdata 10.5Mb
* 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 ... NOTE
annotateOffTargets: no visible binding for global variable
'offTarget_Start'
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
'seqlevelsStyle<-'
annotateOffTargets: no visible global function definition for 'genes'
annotateOffTargets: no visible global function definition for 'toTable'
getPeaks: no visible binding for global variable 'adjusted.p.value'
getPeaks: no visible binding for global variable 'SNratio'
getUniqueCleavageEvents: no visible binding for global variable
'qwidth.first'
getUniqueCleavageEvents: no visible binding for global variable
'qwidth.last'
getUniqueCleavageEvents: no visible binding for global variable
'strand.last'
getUniqueCleavageEvents: no visible binding for global variable
'strand.first'
getUniqueCleavageEvents: no visible binding for global variable
'readName'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
'gRNAPlusPAM'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
'offTarget'
Undefined global functions or variables:
SNratio adjusted.p.value exons gRNAPlusPAM genes offTarget
offTarget_Start qwidth.first qwidth.last readName seqlevelsStyle<-
strand.first strand.last toTable
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:33-35: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:43-45: Dropping empty section \references
prepare_Rd: createBarcodeFasta.Rd:42-43: Dropping empty section \value
prepare_Rd: createBarcodeFasta.Rd:44-46: Dropping empty section \references
prepare_Rd: getUsedBarcodes.Rd:39-41: Dropping empty section \references
* 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
GUIDEseqAnalysis 11.03 0.86 13.17
annotateOffTargets 7.46 0.50 7.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GUIDEseqAnalysis 10.73 0.40 11.16
annotateOffTargets 6.91 0.27 7.24
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/GUIDEseq.Rcheck/00check.log'
for details.
GUIDEseq.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/GUIDEseq_1.12.1.tar.gz && rm -rf GUIDEseq.buildbin-libdir && mkdir GUIDEseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GUIDEseq.buildbin-libdir GUIDEseq_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GUIDEseq_1.12.1.zip && rm GUIDEseq_1.12.1.tar.gz GUIDEseq_1.12.1.zip
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install for i386
* installing *source* package 'GUIDEseq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GUIDEseq'
finding HTML links ... done
GUIDEseq-package html
GUIDEseqAnalysis html
annotateOffTargets html
combineOfftargets html
createBarcodeFasta html
getPeaks html
getUniqueCleavageEvents html
getUsedBarcodes html
mergePlusMinusPeaks html
offTargetAnalysisOfPeakRegions html
peaks.gr html
uniqueCleavageEvents html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GUIDEseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GUIDEseq' as GUIDEseq_1.12.1.zip
* DONE (GUIDEseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GUIDEseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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GUIDEseq.Rcheck/examples_i386/GUIDEseq-Ex.timings
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GUIDEseq.Rcheck/examples_x64/GUIDEseq-Ex.timings
|