Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:39:55 -0400 (Wed, 17 Oct 2018).
Package 764/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
IVAS 2.0.0 Seonggyun Han
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: IVAS |
Version: 2.0.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings IVAS_2.0.0.tar.gz |
StartedAt: 2018-10-17 02:54:36 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 03:00:53 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 376.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: IVAS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings IVAS_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/IVAS.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 'IVAS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'IVAS' version '2.0.0' * 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 '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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-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 10.72 0.13 11.64 sQTLsFinder 10.80 0.03 10.83 ASdb-class 9.76 0.50 10.30 RatioFromFPKM 5.25 0.08 5.33 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed saveBplot 8.17 0.08 10.58 ASdb-class 7.89 0.08 7.97 sQTLsFinder 7.04 0.04 7.07 * 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-3.7-bioc/meat/IVAS.Rcheck/00check.log' for details.
IVAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/IVAS_2.0.0.tar.gz && rm -rf IVAS.buildbin-libdir && mkdir IVAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IVAS.buildbin-libdir IVAS_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL IVAS_2.0.0.zip && rm IVAS_2.0.0.tar.gz IVAS_2.0.0.zip ### ############################################################################## ############################################################################## % 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 76875 100 76875 0 0 1571k 0 --:--:-- --:--:-- --:--:-- 1787k 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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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-3.7-bioc/tmpdir/RtmpGaRCAk/R.INSTALL22cc1a645b9/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 In R CMD INSTALL install for x64 * installing *source* package 'IVAS' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'IVAS' as IVAS_2.0.0.zip * DONE (IVAS) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'IVAS' successfully unpacked and MD5 sums checked In R CMD INSTALL
IVAS.Rcheck/examples_i386/IVAS-Ex.timings
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IVAS.Rcheck/examples_x64/IVAS-Ex.timings
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