| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:34 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1091/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maigesPack 1.65.0 (landing page) Gustavo H. Esteves
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: maigesPack |
| Version: 1.65.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings maigesPack_1.65.0.tar.gz |
| StartedAt: 2023-05-09 20:05:21 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 20:07:50 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 149.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maigesPack.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings maigesPack_1.65.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/maigesPack.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.65.0’
* 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 (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot-methods 7.545 0.109 7.877
normScaleLimma 6.939 0.212 7.172
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘maigesPack_tutorial.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/maigesPack.Rcheck/00check.log’
for details.
maigesPack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL maigesPack ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘maigesPack’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Minfo.c -o Minfo.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c bootstrapT.c -o bootstrapT.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c robustCorr.c -o robustCorr.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c stats.c -o stats.o gcc -shared -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 | 0.003 | 0.000 | 0.003 | |
| activeMod | 1.632 | 0.039 | 1.674 | |
| activeModScoreHTML | 0.787 | 0.036 | 0.822 | |
| activeNet | 3.665 | 0.131 | 3.797 | |
| activeNetScoreHTML | 3.630 | 0.004 | 3.634 | |
| addGeneGrps | 0 | 0 | 0 | |
| addPaths | 0 | 0 | 0 | |
| bootstrapCor | 0.04 | 0.00 | 0.04 | |
| bootstrapMI | 0.171 | 0.000 | 0.172 | |
| bootstrapT | 0.003 | 0.000 | 0.004 | |
| boxplot-methods | 2.793 | 0.204 | 2.997 | |
| bracketMethods | 0.156 | 0.000 | 0.156 | |
| calcA | 0.108 | 0.100 | 0.208 | |
| calcW | 0.120 | 0.096 | 0.215 | |
| classifyKNN | 0.205 | 0.000 | 0.205 | |
| classifyKNNsc | 0.294 | 0.008 | 0.302 | |
| classifyLDA | 0.696 | 0.008 | 0.703 | |
| classifyLDAsc | 1.197 | 0.004 | 1.201 | |
| classifySVM | 0.463 | 0.000 | 0.463 | |
| classifySVMsc | 0.758 | 0.000 | 0.758 | |
| coerce-methods | 0.089 | 0.012 | 0.101 | |
| compCorr | 0 | 0 | 0 | |
| createMaigesRaw | 0.189 | 0.000 | 0.189 | |
| deGenes2by2BootT | 0.402 | 0.004 | 0.406 | |
| deGenes2by2Ttest | 0.228 | 0.012 | 0.240 | |
| deGenes2by2Wilcox | 0.186 | 0.012 | 0.198 | |
| deGenesANOVA | 0.151 | 0.000 | 0.151 | |
| designANOVA | 0.085 | 0.008 | 0.093 | |
| dim-methods | 0.058 | 0.000 | 0.058 | |
| getLabels | 0.060 | 0.008 | 0.068 | |
| hierM | 1.067 | 0.005 | 0.977 | |
| hierMde | 1.712 | 0.032 | 1.743 | |
| image-methods | 1.436 | 0.024 | 1.461 | |
| kmeansM | 1.107 | 0.012 | 1.092 | |
| kmeansMde | 0.597 | 0.000 | 0.596 | |
| loadData | 0.000 | 0.000 | 0.001 | |
| normLoc | 1.202 | 0.012 | 1.214 | |
| normOLIN | 0.06 | 0.00 | 0.06 | |
| normRepLoess | 0.043 | 0.015 | 0.059 | |
| normScaleLimma | 6.939 | 0.212 | 7.172 | |
| normScaleMarray | 1.381 | 0.076 | 1.456 | |
| plot-methods | 7.545 | 0.109 | 7.877 | |
| plotGenePair | 0.088 | 0.008 | 0.096 | |
| print-methods | 0.138 | 0.004 | 0.142 | |
| relNet2TGF | 0.114 | 0.008 | 0.121 | |
| relNetworkB | 2.231 | 0.020 | 2.251 | |
| relNetworkM | 0.075 | 0.012 | 0.088 | |
| robustCorr | 0.001 | 0.000 | 0.001 | |
| selSpots | 0.199 | 0.007 | 0.206 | |
| show-methods | 0.141 | 0.000 | 0.140 | |
| somM | 1.199 | 0.024 | 1.204 | |
| somMde | 0.332 | 0.004 | 0.335 | |
| summarizeReplicates | 1.473 | 0.000 | 1.473 | |
| summary-methods | 0.122 | 0.004 | 0.127 | |
| tableClass | 0.567 | 0.012 | 0.579 | |
| tablesDE | 4.855 | 0.128 | 4.983 | |