Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:21:44 -0400 (Thu, 12 Apr 2018).
Package 657/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
HiTC 1.22.1 Nicolas Servant
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: HiTC |
Version: 1.22.1 |
Command: rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.22.1.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.22.1.tar.gz |
StartedAt: 2018-04-12 00:43:32 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:50:10 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 398.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HiTC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.22.1.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HiTC.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'HiTC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'HiTC' version '1.22.1' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'HiTC' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpojIuhn/R.INSTALL22344a945ed/HiTC/man/import.my5C.Rd:36: missing file link 'import' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HiTC.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 ... NOTE directionalityIndex: no visible global function definition for 'subjectHits' directionalityIndex: no visible global function definition for 'queryHits' getBlocsIndex: no visible global function definition for 'Rle' getExpectedCountsMean: no visible global function definition for 'Rle' normLGF: no visible global function definition for 'glm.nb' slidingWindow: no visible binding for global variable 'consV' splitCombinedContacts : <anonymous>: no visible global function definition for 'seqlevels<-' divide,HTCexp-HTCexp: no visible global function definition for 'queryHits' divide,HTCexp-HTCexp: no visible global function definition for 'subjectHits' isBinned,HTCexp: no visible global function definition for 'countMatches' substract,HTCexp-HTCexp: no visible global function definition for 'queryHits' substract,HTCexp-HTCexp: no visible global function definition for 'subjectHits' Undefined global functions or variables: Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed directionalityIndex 47.72 0.51 51.47 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed directionalityIndex 51.01 0.41 51.43 HTCexp-class 5.35 0.09 5.44 * 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HiTC.Rcheck/00check.log' for details.
HiTC.Rcheck/00install.out
install for i386 * installing *source* package 'HiTC' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'HiTC' finding HTML links ... done CQC html HTCexp-class html HTClist-class html HiTC-internal html Nora_5C html binningC html directionalityIndex html discretize html export.my5C html exportC html extractRegion html getAnnotatedRestrictionSites html getExpectedCounts html getPearsonMap html getRestrictionFragmentsPerChromosome html import.my5C html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpojIuhn/R.INSTALL22344a945ed/HiTC/man/import.my5C.Rd:36: missing file link 'import' importC html intervalsDist html mapC html normICE html normLGF html pca.hic html removeIntervals html setGenomicFeatures html setIntervalScale html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'HiTC' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'HiTC' as HiTC_1.22.1.zip * DONE (HiTC) In R CMD INSTALL In R CMD INSTALL
HiTC.Rcheck/examples_i386/HiTC-Ex.timings
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HiTC.Rcheck/examples_x64/HiTC-Ex.timings
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