| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-03 02:36:06 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1071/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maigesPack 1.63.0 (landing page) Gustavo H. Esteves
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: maigesPack |
| Version: 1.63.0 |
| 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/library --timings maigesPack_1.63.0.tar.gz |
| StartedAt: 2023-02-02 11:27:34 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 11:30:23 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 169.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maigesPack.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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/library --timings maigesPack_1.63.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/maigesPack.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.63.0’
* 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 8.304 0.148 9.756
normScaleLimma 6.853 0.128 7.121
tablesDE 4.930 0.088 5.740
* 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/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/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c Minfo.c -o Minfo.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c robustCorr.c -o robustCorr.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c stats.c -o stats.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-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 | 0.003 | 0.000 | 0.003 | |
| activeMod | 1.645 | 0.023 | 1.671 | |
| activeModScoreHTML | 0.770 | 0.008 | 0.779 | |
| activeNet | 3.836 | 0.015 | 3.858 | |
| activeNetScoreHTML | 3.785 | 0.008 | 3.799 | |
| addGeneGrps | 0 | 0 | 0 | |
| addPaths | 0.001 | 0.000 | 0.000 | |
| bootstrapCor | 0.041 | 0.000 | 0.041 | |
| bootstrapMI | 0.165 | 0.000 | 0.164 | |
| bootstrapT | 0.003 | 0.000 | 0.003 | |
| boxplot-methods | 2.906 | 0.128 | 3.072 | |
| bracketMethods | 0.152 | 0.000 | 0.152 | |
| calcA | 0.112 | 0.080 | 0.192 | |
| calcW | 0.123 | 0.068 | 0.191 | |
| classifyKNN | 0.216 | 0.000 | 0.218 | |
| classifyKNNsc | 0.313 | 0.004 | 0.319 | |
| classifyLDA | 0.710 | 0.012 | 0.730 | |
| classifyLDAsc | 1.211 | 0.000 | 1.215 | |
| classifySVM | 0.455 | 0.004 | 0.459 | |
| classifySVMsc | 0.770 | 0.004 | 0.775 | |
| coerce-methods | 0.080 | 0.020 | 0.101 | |
| compCorr | 0 | 0 | 0 | |
| createMaigesRaw | 0.205 | 0.000 | 0.205 | |
| deGenes2by2BootT | 0.409 | 0.004 | 0.414 | |
| deGenes2by2Ttest | 0.216 | 0.000 | 0.216 | |
| deGenes2by2Wilcox | 0.219 | 0.004 | 0.223 | |
| deGenesANOVA | 0.148 | 0.000 | 0.149 | |
| designANOVA | 0.101 | 0.000 | 0.101 | |
| dim-methods | 0.055 | 0.004 | 0.059 | |
| getLabels | 0.057 | 0.008 | 0.065 | |
| hierM | 1.070 | 0.012 | 1.047 | |
| hierMde | 1.759 | 0.016 | 1.820 | |
| image-methods | 1.772 | 0.008 | 1.784 | |
| kmeansM | 1.117 | 0.028 | 1.286 | |
| kmeansMde | 0.309 | 0.008 | 0.333 | |
| loadData | 0 | 0 | 0 | |
| normLoc | 1.200 | 0.012 | 1.232 | |
| normOLIN | 0.050 | 0.008 | 0.058 | |
| normRepLoess | 0.058 | 0.000 | 0.058 | |
| normScaleLimma | 6.853 | 0.128 | 7.121 | |
| normScaleMarray | 1.404 | 0.048 | 1.670 | |
| plot-methods | 8.304 | 0.148 | 9.756 | |
| plotGenePair | 0.096 | 0.004 | 0.099 | |
| print-methods | 0.123 | 0.004 | 0.127 | |
| relNet2TGF | 0.115 | 0.008 | 0.123 | |
| relNetworkB | 2.279 | 0.000 | 2.279 | |
| relNetworkM | 0.083 | 0.008 | 0.091 | |
| robustCorr | 0.001 | 0.000 | 0.001 | |
| selSpots | 0.214 | 0.012 | 0.226 | |
| show-methods | 0.134 | 0.008 | 0.159 | |
| somM | 1.222 | 0.017 | 1.658 | |
| somMde | 0.347 | 0.008 | 0.425 | |
| summarizeReplicates | 1.846 | 0.008 | 1.874 | |
| summary-methods | 0.116 | 0.016 | 0.133 | |
| tableClass | 0.604 | 0.000 | 0.713 | |
| tablesDE | 4.930 | 0.088 | 5.740 | |