Seonggyun Han
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/IVAS |
| Branch: master |
| Last Commit: 5121735 |
| Last Changed Date: 2019-01-04 13:36:40 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:22:35 -0400 (Tue, 09 Apr 2019).
| Package 832/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IVAS 2.3.1 Seonggyun Han
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: IVAS |
| Version: 2.3.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IVAS_2.3.1.tar.gz |
| StartedAt: 2019-04-09 03:47:25 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:53:36 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 371.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IVAS.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IVAS_2.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IVAS.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IVAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IVAS' version '2.3.1'
* 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 'IVAS' can be installed ... WARNING
Found the following significant warnings:
Note: next used in wrong context: no loop is visible
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/RatioFromFPKM.Rd:46: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/Splicingfinder.Rd:41: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/chrseparate.Rd:31: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/findAlternative.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/findAlternative.Rd:45: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/findOversnp.Rd:29: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IVAS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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
saveBplot 8.45 0.16 10.10
ASdb-class 7.69 0.56 8.31
sQTLsFinder 6.83 0.08 6.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ASdb-class 9.31 0.16 9.47
sQTLsFinder 8.03 0.03 8.08
saveBplot 7.86 0.07 8.69
* 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-3.9-bioc/meat/IVAS.Rcheck/00check.log'
for details.
IVAS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IVAS_2.3.1.tar.gz && rm -rf IVAS.buildbin-libdir && mkdir IVAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IVAS.buildbin-libdir IVAS_2.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IVAS_2.3.1.zip && rm IVAS_2.3.1.tar.gz IVAS_2.3.1.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 76900 100 76900 0 0 328k 0 --:--:-- --:--:-- --:--:-- 336k
install for i386
* installing *source* package 'IVAS' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: next used in wrong context: no loop is visible
** help
*** installing help indices
converting help for package 'IVAS'
finding HTML links ... done
ASdb-class html
CalSigSNP html
IVAS-deprecated html
IVAS-package html
MsqtlFinder html
RatioFromFPKM html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/RatioFromFPKM.Rd:46: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Splicingfinder html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/Splicingfinder.Rd:41: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
calSignificant html
chrseparate html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/chrseparate.Rd:31: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
findAlternative html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/findAlternative.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/findAlternative.Rd:45: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
findOversnp html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpsz2pLP/R.INSTALL17b06a0e5a5c/IVAS/man/findOversnp.Rd:29: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
sQTLsFinder html
sampleexp html
samplesnp html
samplesnplocus html
saveBplot html
sqtlfinder html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'IVAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IVAS' as IVAS_2.3.1.zip
* DONE (IVAS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IVAS' successfully unpacked and MD5 sums checked
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IVAS.Rcheck/examples_i386/IVAS-Ex.timings
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IVAS.Rcheck/examples_x64/IVAS-Ex.timings
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