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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GlobalAncova package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GlobalAncova.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 777/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GlobalAncova 4.10.0 (landing page) Manuela Hummel
| 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: GlobalAncova |
Version: 4.10.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GlobalAncova.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GlobalAncova_4.10.0.tar.gz |
StartedAt: 2021-10-14 23:52:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:56:44 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 232.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GlobalAncova.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GlobalAncova.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GlobalAncova_4.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GlobalAncova.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 'GlobalAncova/DESCRIPTION' ... OK * this is package 'GlobalAncova' version '4.10.0' * 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 'GlobalAncova' 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 ... NOTE Package in Depends field not imported from: 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .nPerms: no visible global function definition for 'terms' .onAttach: no visible global function definition for 'addVigs2WinMenu' .pAsymptotic: no visible global function definition for 'qnorm' .pAsymptotic: no visible global function definition for 'pchisq' .pGAapprox: no visible global function definition for 'model.matrix' GABroad: no visible global function definition for 'is' GABroad: no visible binding for global variable 'collectionType' GABroad: no visible binding for global variable 'geneIds' GABroad: no visible global function definition for 'p.adjust' GAGO: no visible binding for global variable 'Ontology' GAGO: no visible global function definition for 'is' GAGO: no visible global function definition for 'p.adjust' GAGO : <anonymous>: no visible global function definition for 'is' Gsquared: no visible global function definition for 'glm' Gsquared: no visible binding for global variable 'multinomial' Gsquared: no visible global function definition for 'pchisq' Gsquared: no visible global function definition for 'qchisq' Plot.all: no visible global function definition for 'par' Plot.all: no visible global function definition for 'layout' Plot.features: no visible global function definition for 'barplot' Plot.sequential: no visible global function definition for 'par' Plot.sequential: no visible global function definition for 'barplot' Plot.sequential: no visible global function definition for 'legend' Plot.sequential: no visible global function definition for 'axis' Tperm.catcat: no visible global function definition for 'pchisq' Tperm.catcat: no visible global function definition for 'qchisq' coldend: no visible global function definition for 'is.leaf' decomp.ssq: no visible global function definition for 'model.matrix' decomp.ssq: no visible global function definition for 'as.formula' decomp.ssq: no visible global function definition for 'anova' decomp.ssq: no visible global function definition for 'lm' decomp.ssq: no visible global function definition for 'pf' decomp.ssq.genewise: no visible global function definition for 'model.matrix' decomp.ssq.genewise: no visible global function definition for 'as.formula' decomp.ssq.genewise: no visible global function definition for 'anova' decomp.ssq.genewise: no visible global function definition for 'lm' decomp.ssq.genewise: no visible global function definition for 'pf' devtest: no visible global function definition for 'formula' devtest: no visible global function definition for 'na.omit' devtest: no visible global function definition for 'pchisq' devtest: no visible global function definition for 'qchisq' expr.test: no visible global function definition for 'terms' expr.test: no visible global function definition for 'model.matrix' gGAteststats: no visible global function definition for 'terms' gGAteststats: no visible global function definition for 'complete.cases' gGAteststats : <anonymous>: no visible global function definition for 'na.omit' gGAteststats: no visible global function definition for 'model.matrix' gGlobalAncova.hierarchical: no visible global function definition for 'new' getdev: no visible binding for global variable 'nobs' getdev: no visible global function definition for 'glm.fit' getdev: no visible global function definition for 'binomial' group2formula: no visible global function definition for 'as.formula' hiertest: no visible global function definition for 'na.omit' horizontal.bars: no visible global function definition for 'plot.new' horizontal.bars: no visible global function definition for 'strwidth' horizontal.bars: no visible global function definition for 'par' horizontal.bars: no visible global function definition for 'rect' horizontal.bars: no visible global function definition for 'box' horizontal.bars: no visible global function definition for 'axis' my.colors: no visible global function definition for 'rainbow' my.colors: no visible global function definition for 'rgb' pair.compare: no visible global function definition for 'model.matrix' plot.ssq.all: no visible global function definition for 'par' plot.ssq.all: no visible global function definition for 'barplot' plot.ssq.all: no visible global function definition for 'axis' plot.ssq.genewise2: no visible global function definition for 'par' plot.ssq.genewise2: no visible global function definition for 'barplot' plot.ssq.genewise2: no visible global function definition for 'legend' plot.ssq.genewise2: no visible global function definition for 'axis' plotallgenes: no visible global function definition for 'par' plotallgenes: no visible global function definition for 'barplot' plotallgenes: no visible global function definition for 'lines' plotgenes: no visible global function definition for 'palette' plotgenes: no visible global function definition for 'rgb' plotgenes: no visible global function definition for 'lines' plotgenes: no visible global function definition for 'legend' plotgenes2: no visible global function definition for 'par' plotgenes2: no visible global function definition for 'barplot' plotgenes2: no visible global function definition for 'axis' plotgenes2: no visible global function definition for 'lines' plotgenes2: no visible global function definition for 'rect' plotsubjects: no visible global function definition for 'palette' plotsubjects: no visible global function definition for 'rgb' plotsubjects: no visible global function definition for 'legend' reduSQ: no visible global function definition for 'model.matrix' GlobalAncova.closed,matrix-list-formula-missing-ANY-missing-missing-character: no visible global function definition for 'model.matrix' GlobalAncova,matrix-formula-missing-ANY-missing-missing-character: no visible global function definition for 'model.matrix' Plot.genes,matrix-formula-missing-ANY-missing-missing-character: no visible global function definition for 'model.matrix' Plot.subjects,matrix-formula-missing-ANY-missing-missing-character: no visible global function definition for 'model.matrix' pGAapprox,matrix-formula-missing-ANY-missing-missing-character: no visible global function definition for 'model.matrix' Undefined global functions or variables: Ontology addVigs2WinMenu anova as.formula axis barplot binomial box collectionType complete.cases formula geneIds glm glm.fit is is.leaf layout legend lines lm model.matrix multinomial na.omit new nobs p.adjust palette par pchisq pf plot.new qchisq qnorm rainbow rect rgb strwidth terms Consider adding importFrom("grDevices", "palette", "rainbow", "rgb") importFrom("graphics", "axis", "barplot", "box", "layout", "legend", "lines", "par", "plot.new", "rect", "strwidth") importFrom("methods", "is", "new") importFrom("stats", "anova", "as.formula", "binomial", "complete.cases", "formula", "glm", "glm.fit", "is.leaf", "lm", "model.matrix", "na.omit", "nobs", "p.adjust", "pchisq", "pf", "qchisq", "qnorm", "terms") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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-3.13-bioc/R/library/GlobalAncova/libs/i386/GlobalAncova.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'putchar', possibly from 'putchar' (C) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/GlobalAncova/libs/x64/GlobalAncova.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'putchar', possibly from 'putchar' (C) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) 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 ** running examples for arch 'x64' ... 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GlobalAncova.Rcheck/00check.log' for details.
GlobalAncova.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GlobalAncova_4.10.0.tar.gz && rm -rf GlobalAncova.buildbin-libdir && mkdir GlobalAncova.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GlobalAncova.buildbin-libdir GlobalAncova_4.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GlobalAncova_4.10.0.zip && rm GlobalAncova_4.10.0.tar.gz GlobalAncova_4.10.0.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 2 606k 2 13527 0 0 112k 0 0:00:05 --:--:-- 0:00:05 112k 100 606k 100 606k 0 0 1644k 0 --:--:-- --:--:-- --:--:-- 1644k install for i386 * installing *source* package 'GlobalAncova' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GlobalAncova.c -o GlobalAncova.o GlobalAncova.c: In function 'permut_withFperm': GlobalAncova.c:166:8: warning: 'ord_perm' may be used uninitialized in this function [-Wmaybe-uninitialized] int *ord_perm ; ^~~~~~~~ GlobalAncova.c: In function 'permut': GlobalAncova.c:268:8: warning: 'ord_perm' may be used uninitialized in this function [-Wmaybe-uninitialized] int *ord_perm ; ^~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ludcmp.c -o ludcmp.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix.c -o matrix.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GlobalAncova.dll tmp.def GlobalAncova.o ludcmp.o matrix.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GlobalAncova.buildbin-libdir/00LOCK-GlobalAncova/00new/GlobalAncova/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GlobalAncova' finding HTML links ... done GAhier-class html GlobalAncova-methods html GlobalAncova html GlobalAncova.closed-methods html GlobalAncova.closed html GlobalAncova.decomp html Plot.all html Plot.features html Plot.genes-methods html Plot.genes html Plot.sequential html Plot.subjects-methods html Plot.subjects html bindata html colon.normal html colon.pheno html colon.tumour html gGlobalAncova html gGlobalAncova.hierarchical html genesettesting html pair.compare html pathways html phenodata html vantVeer 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 'GlobalAncova' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GlobalAncova.c -o GlobalAncova.o GlobalAncova.c: In function 'permut_withFperm': GlobalAncova.c:166:8: warning: 'ord_perm' may be used uninitialized in this function [-Wmaybe-uninitialized] int *ord_perm ; ^~~~~~~~ GlobalAncova.c: In function 'permut': GlobalAncova.c:268:8: warning: 'ord_perm' may be used uninitialized in this function [-Wmaybe-uninitialized] int *ord_perm ; ^~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ludcmp.c -o ludcmp.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix.c -o matrix.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GlobalAncova.dll tmp.def GlobalAncova.o ludcmp.o matrix.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GlobalAncova.buildbin-libdir/GlobalAncova/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'GlobalAncova' as GlobalAncova_4.10.0.zip * DONE (GlobalAncova) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'GlobalAncova' successfully unpacked and MD5 sums checked
GlobalAncova.Rcheck/examples_i386/GlobalAncova-Ex.timings
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GlobalAncova.Rcheck/examples_x64/GlobalAncova-Ex.timings
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