Lihua Julie Zhu
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/REDseq |
| Branch: RELEASE_3_7 |
| Last Commit: d06d746 |
| Last Changed Date: 2018-04-30 10:35:18 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:24 -0400 (Wed, 17 Oct 2018).
| Package 1214/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| REDseq 1.26.0 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: REDseq |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings REDseq_1.26.0.tar.gz |
| StartedAt: 2018-10-17 04:20:12 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:26:12 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 360.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: REDseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings REDseq_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/REDseq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'REDseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REDseq' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'BSgenome.Celegans.UCSC.ce2' 'multtest' 'Biostrings'
'BSgenome' 'ChIPpeakAnno'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'REDseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocGenerics' 'Biostrings' 'ChIPpeakAnno' 'multtest'
A package should be listed in only one of these fields.
* 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 ... NOTE
Package in Depends field not imported from: 'BSgenome.Celegans.UCSC.ce2'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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
buildREmap 7.10 0.24 7.33
searchPattern 4.98 0.18 5.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
buildREmap 6.82 0.17 6.98
searchPattern 5.18 0.11 5.30
* 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-3.7-bioc/meat/REDseq.Rcheck/00check.log'
for details.
REDseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/REDseq_1.26.0.tar.gz && rm -rf REDseq.buildbin-libdir && mkdir REDseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=REDseq.buildbin-libdir REDseq_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL REDseq_1.26.0.zip && rm REDseq_1.26.0.tar.gz REDseq_1.26.0.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 31744 100 31744 0 0 524k 0 --:--:-- --:--:-- --:--:-- 596k
install for i386
* installing *source* package 'REDseq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** help
*** installing help indices
converting help for package 'REDseq'
finding HTML links ... done
REDseq-package html
assignSeq2REsite html
binom.test.REDseq html
buildREmap html
compareREDseq html
distanceHistSeq2RE html
example.REDseq html
example.assignedREDseq html
example.map html
plotCutDistribution html
searchPattern html
summarizeByRE html
summarizeBySeq html
writeHits html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
In R CMD INSTALL
install for x64
* installing *source* package 'REDseq' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
* MD5 sums
packaged installation of 'REDseq' as REDseq_1.26.0.zip
* DONE (REDseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'REDseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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REDseq.Rcheck/examples_i386/REDseq-Ex.timings
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REDseq.Rcheck/examples_x64/REDseq-Ex.timings
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