Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:33:52 -0400 (Wed, 16 Oct 2019).
Package 257/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ChIPComp 1.14.0 Li Chen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: ChIPComp |
Version: 1.14.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPComp.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPComp_1.14.0.tar.gz |
StartedAt: 2019-10-16 02:35:55 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:41:29 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 333.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPComp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPComp.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPComp_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPComp.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChIPComp/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChIPComp' version '1.14.0' * 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 'ChIPComp' 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 ChIPComp: no visible global function definition for 'queryHits' ChIPComp: no visible global function definition for 'pnorm' findCommonPeak: no visible global function definition for 'ppois' getCTCounts: no visible global function definition for 'seqlevels' getCTCounts: no visible global function definition for 'seqnames' getCTCounts: no visible global function definition for 'subjectHits' getCTCounts: no visible global function definition for 'queryHits' makeConf: no visible global function definition for 'read.csv' makeConf: no visible global function definition for 'model.matrix' makePeakSet: no visible global function definition for 'subjectHits' plot.ChIPComp : mypar: no visible global function definition for 'par' plot.ChIPComp: no visible global function definition for 'lm' plot.ChIPComp: no visible global function definition for 'coef' plot.ChIPComp: no visible global function definition for 'plot' plot.ChIPComp: no visible global function definition for 'smooth.spline' plot.ChIPComp: no visible global function definition for 'lines' regress: no visible global function definition for 'lm' regress: no visible global function definition for 'coef' regress: no visible global function definition for 'resid' regress: no visible global function definition for 'smooth.spline' regress: no visible global function definition for 'predict' rmdup: no visible global function definition for 'qbinom' Undefined global functions or variables: coef lines lm model.matrix par plot pnorm ppois predict qbinom queryHits read.csv resid seqlevels seqnames smooth.spline subjectHits Consider adding importFrom("graphics", "lines", "par", "plot") importFrom("stats", "coef", "lm", "model.matrix", "pnorm", "ppois", "predict", "qbinom", "resid", "smooth.spline") importFrom("utils", "read.csv") 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ChIPComp/libs/i386/ChIPComp.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ChIPComp/libs/x64/ChIPComp.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed makeCountSet 14.36 1.5 16.72 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed makeCountSet 10.38 1.16 11.53 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' OK * 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-3.9-bioc/meat/ChIPComp.Rcheck/00check.log' for details.
ChIPComp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChIPComp_1.14.0.tar.gz && rm -rf ChIPComp.buildbin-libdir && mkdir ChIPComp.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPComp.buildbin-libdir ChIPComp_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChIPComp_1.14.0.zip && rm ChIPComp_1.14.0.tar.gz ChIPComp_1.14.0.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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 434k 100 434k 0 0 6362k 0 --:--:-- --:--:-- --:--:-- 6897k install for i386 * installing *source* package 'ChIPComp' ... ** using staged installation ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mva.c -o mva.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o ChIPComp.dll tmp.def mva.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPComp.buildbin-libdir/00LOCK-ChIPComp/00new/ChIPComp/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ChIPComp' finding HTML links ... done ChIPComp-package html ChIPComp html makeConf html makeCountSet html plot html print html seqData 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 'ChIPComp' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mva.c -o mva.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o ChIPComp.dll tmp.def mva.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPComp.buildbin-libdir/ChIPComp/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ChIPComp' as ChIPComp_1.14.0.zip * DONE (ChIPComp) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'ChIPComp' successfully unpacked and MD5 sums checked
ChIPComp.Rcheck/tests_i386/runTests.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("ChIPComp") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Making peak list...... Making ip counts...... Making control counts...... RUNIT TEST PROTOCOL -- Wed Oct 16 02:41:03 2019 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : ChIPComp RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 22.35 1.92 24.26 |
ChIPComp.Rcheck/tests_x64/runTests.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("ChIPComp") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Making peak list...... Making ip counts...... Making control counts...... RUNIT TEST PROTOCOL -- Wed Oct 16 02:41:24 2019 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : ChIPComp RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 19.18 1.23 20.42 |
ChIPComp.Rcheck/examples_i386/ChIPComp-Ex.timings
|
ChIPComp.Rcheck/examples_x64/ChIPComp-Ex.timings
|