Gustavo H. Esteves
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/maigesPack |
| Branch: RELEASE_3_12 |
| Last Commit: 5910e59 |
| Last Changed Date: 2020-10-27 10:32:10 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:07 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the maigesPack package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 992/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maigesPack 1.54.0 (landing page) Gustavo H. Esteves
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: maigesPack |
| Version: 1.54.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings maigesPack_1.54.0.tar.gz |
| StartedAt: 2021-05-06 03:02:16 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:04:30 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 133.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maigesPack.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings maigesPack_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/maigesPack.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.54.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
plot-methods 8.016 0.100 8.667
normScaleLimma 7.364 0.184 7.755
* 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-3.12-bioc/meat/maigesPack.Rcheck/00check.log’
for details.
maigesPack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL maigesPack ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘maigesPack’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Minfo.c -o Minfo.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c robustCorr.c -o robustCorr.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c stats.c -o stats.o gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/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 | 0.004 | 0.000 | 0.004 | |
| activeMod | 1.804 | 0.008 | 1.815 | |
| activeModScoreHTML | 0.884 | 0.008 | 0.897 | |
| activeNet | 3.472 | 0.012 | 3.492 | |
| activeNetScoreHTML | 4.028 | 0.008 | 4.044 | |
| addGeneGrps | 0 | 0 | 0 | |
| addPaths | 0 | 0 | 0 | |
| bootstrapCor | 0.048 | 0.000 | 0.047 | |
| bootstrapMI | 0.220 | 0.000 | 0.223 | |
| bootstrapT | 0.004 | 0.000 | 0.004 | |
| boxplot-methods | 2.324 | 0.140 | 2.476 | |
| bracketMethods | 0.200 | 0.004 | 0.206 | |
| calcA | 0.156 | 0.068 | 0.227 | |
| calcW | 0.128 | 0.052 | 0.178 | |
| classifyKNN | 0.164 | 0.000 | 0.166 | |
| classifyKNNsc | 0.332 | 0.000 | 0.331 | |
| classifyLDA | 0.984 | 0.000 | 0.982 | |
| classifyLDAsc | 1.672 | 0.004 | 1.678 | |
| classifySVM | 0.408 | 0.000 | 0.408 | |
| classifySVMsc | 0.596 | 0.000 | 0.598 | |
| coerce-methods | 0.136 | 0.008 | 0.145 | |
| compCorr | 0 | 0 | 0 | |
| createMaigesRaw | 0.300 | 0.000 | 0.301 | |
| deGenes2by2BootT | 0.572 | 0.000 | 0.570 | |
| deGenes2by2Ttest | 0.316 | 0.004 | 0.319 | |
| deGenes2by2Wilcox | 0.296 | 0.000 | 0.298 | |
| deGenesANOVA | 0.204 | 0.016 | 0.218 | |
| designANOVA | 0.140 | 0.000 | 0.142 | |
| dim-methods | 0.096 | 0.000 | 0.092 | |
| getLabels | 0.096 | 0.012 | 0.111 | |
| hierM | 1.572 | 0.000 | 1.502 | |
| hierMde | 1.748 | 0.036 | 1.789 | |
| image-methods | 1.612 | 0.024 | 1.639 | |
| kmeansM | 1.456 | 0.032 | 1.492 | |
| kmeansMde | 0.384 | 0.004 | 0.389 | |
| loadData | 0 | 0 | 0 | |
| normLoc | 2.196 | 0.004 | 2.201 | |
| normOLIN | 0.096 | 0.000 | 0.094 | |
| normRepLoess | 0.096 | 0.000 | 0.097 | |
| normScaleLimma | 7.364 | 0.184 | 7.755 | |
| normScaleMarray | 1.084 | 0.012 | 1.095 | |
| plot-methods | 8.016 | 0.100 | 8.667 | |
| plotGenePair | 0.096 | 0.004 | 0.100 | |
| print-methods | 0.124 | 0.000 | 0.122 | |
| relNet2TGF | 0.116 | 0.008 | 0.124 | |
| relNetworkB | 1.684 | 0.004 | 1.690 | |
| relNetworkM | 0.096 | 0.004 | 0.100 | |
| robustCorr | 0.000 | 0.000 | 0.001 | |
| selSpots | 0.224 | 0.016 | 0.241 | |
| show-methods | 0.176 | 0.004 | 0.180 | |
| somM | 1.612 | 0.012 | 1.658 | |
| somMde | 0.320 | 0.008 | 0.329 | |
| summarizeReplicates | 1.164 | 0.024 | 1.192 | |
| summary-methods | 0.184 | 0.008 | 0.194 | |
| tableClass | 0.656 | 0.008 | 0.665 | |
| tablesDE | 3.124 | 0.056 | 3.186 | |