Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the CODEX package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CODEX.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 358/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CODEX 1.24.0 (landing page) Yuchao Jiang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: CODEX |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CODEX_1.24.0.tar.gz |
StartedAt: 2021-10-14 21:22:46 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:28:41 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 354.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CODEX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CODEX_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CODEX.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CODEX/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CODEX' version '1.24.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Rsamtools', 'GenomeInfoDb', 'BSgenome.Hsapiens.UCSC.hg19', 'IRanges', 'Biostrings', 'S4Vectors' 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 'CODEX' can be installed ... OK * 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 choiceofK: no visible global function definition for 'pdf' choiceofK: no visible global function definition for 'par' choiceofK: no visible global function definition for 'dev.off' getbambed: no visible global function definition for 'read.table' normalize : <anonymous>: no visible global function definition for 'smooth.spline' normalize : <anonymous>: no visible global function definition for 'predict' normalize: no visible global function definition for 'glm' normalize: no visible binding for global variable 'poisson' normalize: no visible global function definition for 'lm' normalize2 : <anonymous>: no visible global function definition for 'smooth.spline' normalize2 : <anonymous>: no visible global function definition for 'predict' normalize2: no visible global function definition for 'glm' normalize2: no visible binding for global variable 'poisson' normalize2: no visible global function definition for 'lm' Undefined global functions or variables: dev.off glm lm par pdf poisson predict read.table smooth.spline Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "par") importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline") importFrom("utils", "read.table") to your NAMESPACE file. * 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 LazyData ... 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 (user + system) or elapsed time > 5s user system elapsed normalize 20.16 0.04 20.20 normalize2 16.62 0.04 16.66 getcoverage 9.94 0.54 10.48 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed normalize 23.01 0.02 23.03 normalize2 19.05 0.00 19.05 getcoverage 9.93 0.33 10.25 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CODEX.Rcheck/00check.log' for details.
CODEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CODEX_1.24.0.tar.gz && rm -rf CODEX.buildbin-libdir && mkdir CODEX.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CODEX.buildbin-libdir CODEX_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CODEX_1.24.0.zip && rm CODEX_1.24.0.tar.gz CODEX_1.24.0.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 734k 100 734k 0 0 1922k 0 --:--:-- --:--:-- --:--:-- 1926k install for i386 * installing *source* package 'CODEX' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CODEX' finding HTML links ... done CODEX-package html bambedObjDemo html choiceofK html coverageObjDemo html gcDemo html getbambed html getcoverage html getgc html getmapp html mappDemo html mapp_ref html mappability html normObjDemo html normalize html normalize2 html qc html qcObjDemo html segment 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 'CODEX' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'CODEX' as CODEX_1.24.0.zip * DONE (CODEX) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'CODEX' successfully unpacked and MD5 sums checked
CODEX.Rcheck/examples_i386/CODEX-Ex.timings
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CODEX.Rcheck/examples_x64/CODEX-Ex.timings
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