Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:52 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1138/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maigesPack 1.66.0 (landing page) Gustavo H. Esteves
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the maigesPack package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maigesPack.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: maigesPack |
Version: 1.66.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings maigesPack_1.66.0.tar.gz |
StartedAt: 2023-11-02 11:48:20 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 11:50:02 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 102.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: maigesPack.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings maigesPack_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/maigesPack.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maigesPack/DESCRIPTION’ ... OK * this is package ‘maigesPack’ version ‘1.66.0’ * 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 ... 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 for sufficient/correct file permissions ... OK * checking whether package ‘maigesPack’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘OLIN’ ‘annotate’ ‘rgl’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE activeMod: no visible global function definition for ‘sessionInfo’ activeModScoreHTML: no visible binding for global variable ‘data’ activeNet: no visible global function definition for ‘sessionInfo’ activeNetScoreHTML: no visible binding for global variable ‘data’ blackBlue: no visible global function definition for ‘col2rgb’ blackBlue: no visible global function definition for ‘rgb’ classifyKNN: no visible global function definition for ‘sessionInfo’ classifyKNNsc: no visible global function definition for ‘sessionInfo’ classifyLDA: no visible global function definition for ‘sessionInfo’ classifyLDAsc: no visible global function definition for ‘sessionInfo’ classifySVM: no visible global function definition for ‘sessionInfo’ classifySVMsc: no visible global function definition for ‘sessionInfo’ createMaigesRaw: no visible global function definition for ‘sessionInfo’ createTDMS: no visible global function definition for ‘write.table’ deGenes2by2BootT: no visible global function definition for ‘sessionInfo’ deGenes2by2Ttest: no visible global function definition for ‘sessionInfo’ deGenes2by2Wilcox: no visible global function definition for ‘sessionInfo’ deGenesANOVA: no visible global function definition for ‘sessionInfo’ designANOVA: no visible global function definition for ‘sessionInfo’ greenRed: no visible global function definition for ‘col2rgb’ greenRed: no visible global function definition for ‘rgb’ loadData: no visible global function definition for ‘read.table’ loadData: no visible global function definition for ‘sessionInfo’ normLoc: no visible global function definition for ‘sessionInfo’ normOLIN: no visible global function definition for ‘sessionInfo’ normRepLoess: no visible global function definition for ‘sessionInfo’ normScaleLimma: no visible global function definition for ‘sessionInfo’ normScaleMarray: no visible global function definition for ‘sessionInfo’ print.maiges: no visible global function definition for ‘str’ print.maigesANOVA: no visible global function definition for ‘str’ print.maigesPreRaw: no visible global function definition for ‘str’ print.maigesRaw: no visible global function definition for ‘str’ relNet2TGF.maigesRelNetB: no visible global function definition for ‘write.table’ relNet2TGF.maigesRelNetM: no visible global function definition for ‘write.table’ relNetworkB: no visible global function definition for ‘sessionInfo’ relNetworkM: no visible global function definition for ‘sessionInfo’ selSpots: no visible global function definition for ‘sessionInfo’ summarizeReplicates: no visible global function definition for ‘sessionInfo’ tableClass: no visible global function definition for ‘write.table’ tablesDE: no visible global function definition for ‘setRepository’ tablesDE: no visible global function definition for ‘write.table’ Undefined global functions or variables: col2rgb data read.table rgb sessionInfo setRepository str write.table Consider adding importFrom("grDevices", "col2rgb", "rgb") importFrom("utils", "data", "read.table", "sessionInfo", "str", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) addPaths.Rd:11: Escaped LaTeX specials: \# checkRd: (-1) loadData.Rd:51: Escaped LaTeX specials: \_ * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘maigesPack-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: normScaleLimma > ### Title: Scale adjust a cDNA Microarray Object > ### Aliases: normScaleLimma > ### Keywords: classes > > ### ** Examples > > ## Loading the dataset > data(gastro) > > ## Doing the scale adjustment from median-absolute-value method (from > ## limma) > gastro.norm = normScaleLimma(gastro.norm, method="scale") > boxplot(gastro.norm) ## To see the efect of adjustment > > ## To do VSN scale adjustment (from vsn package) use the command. Be > ## carefull that this method adjust the variance along A values and not > ## between chips!! > gastro.norm = normScaleLimma(gastro.raw2, method="vsn") Error in normalizeVSN(toNorm) : vsn package required but is not installed (or can't be loaded) Calls: normScaleLimma -> normalizeVSN Execution halted * 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 ERROR, 6 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/maigesPack.Rcheck/00check.log’ for details.
maigesPack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL maigesPack ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘maigesPack’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c Minfo.c -o Minfo.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c robustCorr.c -o robustCorr.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c stats.c -o stats.o gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-maigesPack/00new/maigesPack/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maigesPack)
maigesPack.Rcheck/maigesPack-Ex.timings
name | user | system | elapsed | |
MI | 0.012 | 0.000 | 0.011 | |
activeMod | 1.676 | 0.021 | 1.701 | |
activeModScoreHTML | 0.817 | 0.036 | 0.855 | |
activeNet | 3.935 | 0.140 | 4.082 | |
activeNetScoreHTML | 3.848 | 0.004 | 3.859 | |
addGeneGrps | 0 | 0 | 0 | |
addPaths | 0 | 0 | 0 | |
bootstrapCor | 0.041 | 0.000 | 0.042 | |
bootstrapMI | 0.160 | 0.000 | 0.162 | |
bootstrapT | 0.003 | 0.000 | 0.003 | |
boxplot-methods | 2.871 | 0.112 | 2.990 | |
bracketMethods | 0.132 | 0.020 | 0.152 | |
calcA | 0.113 | 0.068 | 0.181 | |
calcW | 0.114 | 0.080 | 0.195 | |
classifyKNN | 0.204 | 0.008 | 0.213 | |
classifyKNNsc | 0.308 | 0.008 | 0.316 | |
classifyLDA | 0.735 | 0.004 | 0.740 | |
classifyLDAsc | 1.265 | 0.004 | 1.272 | |
classifySVM | 0.454 | 0.011 | 0.467 | |
classifySVMsc | 0.776 | 0.004 | 0.782 | |
coerce-methods | 0.091 | 0.008 | 0.099 | |
compCorr | 0 | 0 | 0 | |
createMaigesRaw | 0.198 | 0.008 | 0.206 | |
deGenes2by2BootT | 0.409 | 0.004 | 0.415 | |
deGenes2by2Ttest | 0.218 | 0.000 | 0.218 | |
deGenes2by2Wilcox | 0.213 | 0.012 | 0.226 | |
deGenesANOVA | 0.148 | 0.000 | 0.149 | |
designANOVA | 0.086 | 0.011 | 0.098 | |
dim-methods | 0.057 | 0.000 | 0.057 | |
getLabels | 0.059 | 0.003 | 0.063 | |
hierM | 1.089 | 0.008 | 1.005 | |
hierMde | 1.749 | 0.020 | 1.773 | |
image-methods | 1.821 | 0.008 | 1.833 | |
kmeansM | 1.117 | 0.036 | 1.132 | |
kmeansMde | 0.314 | 0.008 | 0.321 | |
loadData | 0 | 0 | 0 | |
normLoc | 1.215 | 0.004 | 1.220 | |
normOLIN | 0.048 | 0.008 | 0.056 | |
normRepLoess | 0.058 | 0.000 | 0.057 | |