Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:22:12 -0400 (Wed, 17 Oct 2018).
Package 820/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
maigesPack 1.44.0 Gustavo H. Esteves
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: maigesPack |
Version: 1.44.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings maigesPack_1.44.0.tar.gz |
StartedAt: 2018-10-16 01:37:14 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 01:38:55 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 101.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maigesPack.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings maigesPack_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/maigesPack.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maigesPack/DESCRIPTION’ ... OK * this is package ‘maigesPack’ version ‘1.44.0’ * 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 * 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 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 ... 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed normScaleLimma 10.384 0.208 11.410 plot-methods 5.956 0.408 6.753 * 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: 5 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/maigesPack.Rcheck/00check.log’ for details.
maigesPack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL maigesPack ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘maigesPack’ ... ** libs gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Minfo.c -o Minfo.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c robustCorr.c -o robustCorr.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c stats.c -o stats.o gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/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 * DONE (maigesPack)
maigesPack.Rcheck/maigesPack-Ex.timings
name | user | system | elapsed | |
MI | 0.004 | 0.000 | 0.005 | |
activeMod | 1.072 | 0.056 | 1.148 | |
activeModScoreHTML | 0.472 | 0.028 | 0.506 | |
activeNet | 2.292 | 0.048 | 2.350 | |
activeNetScoreHTML | 2.292 | 0.024 | 2.325 | |
addGeneGrps | 0.000 | 0.000 | 0.001 | |
addPaths | 0 | 0 | 0 | |
bootstrapCor | 0.024 | 0.008 | 0.032 | |
bootstrapMI | 0.148 | 0.000 | 0.151 | |
bootstrapT | 0.000 | 0.000 | 0.003 | |
boxplot-methods | 1.496 | 0.192 | 1.707 | |
bracketMethods | 0.140 | 0.004 | 0.143 | |
calcA | 0.128 | 0.048 | 0.177 | |
calcW | 0.128 | 0.052 | 0.180 | |
classifyKNN | 0.192 | 0.036 | 0.248 | |
classifyKNNsc | 0.232 | 0.056 | 0.300 | |
classifyLDA | 0.528 | 0.056 | 0.599 | |
classifyLDAsc | 0.936 | 0.072 | 1.024 | |
classifySVM | 0.432 | 0.068 | 0.508 | |
classifySVMsc | 0.628 | 0.068 | 0.707 | |
coerce-methods | 0.088 | 0.012 | 0.102 | |
compCorr | 0.000 | 0.000 | 0.001 | |
createMaigesRaw | 0.192 | 0.024 | 0.219 | |
deGenes2by2BootT | 0.376 | 0.024 | 0.410 | |
deGenes2by2Ttest | 0.280 | 0.048 | 0.334 | |
deGenes2by2Wilcox | 0.160 | 0.028 | 0.195 | |
deGenesANOVA | 0.152 | 0.048 | 0.213 | |
designANOVA | 0.096 | 0.032 | 0.134 | |
dim-methods | 0.076 | 0.000 | 0.075 | |
getLabels | 0.096 | 0.016 | 0.113 | |
hierM | 1.092 | 0.052 | 1.049 | |
hierMde | 1.196 | 0.076 | 1.279 | |
image-methods | 0.960 | 0.064 | 1.035 | |
kmeansM | 0.924 | 0.032 | 0.990 | |
kmeansMde | 0.292 | 0.036 | 0.338 | |
loadData | 0.000 | 0.000 | 0.001 | |
normLoc | 1.716 | 0.100 | 1.833 | |
normOLIN | 0.064 | 0.000 | 0.063 | |
normRepLoess | 0.064 | 0.000 | 0.063 | |
normScaleLimma | 10.384 | 0.208 | 11.410 | |
normScaleMarray | 1.128 | 0.180 | 1.318 | |
plot-methods | 5.956 | 0.408 | 6.753 | |
plotGenePair | 0.164 | 0.048 | 0.217 | |
print-methods | 0.144 | 0.012 | 0.155 | |
relNet2TGF | 0.144 | 0.036 | 0.187 | |
relNetworkB | 1.184 | 0.108 | 1.306 | |
relNetworkM | 0.084 | 0.052 | 0.141 | |
robustCorr | 0.000 | 0.000 | 0.001 | |
selSpots | 0.184 | 0.084 | 0.279 | |
show-methods | 0.120 | 0.004 | 0.124 | |
somM | 1.040 | 0.036 | 1.063 | |
somMde | 0.344 | 0.052 | 0.400 | |
summarizeReplicates | 0.992 | 0.108 | 1.114 | |
summary-methods | 0.108 | 0.028 | 0.137 | |
tableClass | 0.456 | 0.044 | 0.504 | |
tablesDE | 2.980 | 0.148 | 3.135 | |