| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-07 20:25 -0400 (Fri, 07 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 1151/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Gustavo H. Esteves
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: maigesPack |
| Version: 1.68.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maigesPack.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings maigesPack_1.68.0.tar.gz |
| StartedAt: 2024-06-06 05:50:55 -0400 (Thu, 06 Jun 2024) |
| EndedAt: 2024-06-06 05:55:11 -0400 (Thu, 06 Jun 2024) |
| EllapsedTime: 255.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maigesPack.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maigesPack.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings maigesPack_1.68.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/maigesPack.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.68.0'
* 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 whether package 'maigesPack' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/maigesPack/libs/x64/maigesPack.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normScaleLimma 6.99 3.84 10.97
plot-methods 4.35 4.60 9.24
tablesDE 3.44 2.79 6.35
boxplot-methods 2.65 2.41 5.11
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/maigesPack.Rcheck/00check.log'
for details.
maigesPack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL maigesPack ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'maigesPack' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Minfo.c -o Minfo.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bootstrapT.c -o bootstrapT.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c robustCorr.c -o robustCorr.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stats.c -o stats.o gcc -shared -s -static-libgcc -o maigesPack.dll tmp.def Minfo.o bootstrapT.o register.o robustCorr.o stats.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-maigesPack/00new/maigesPack/libs/x64 ** 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 Warning in fun(libname, pkgname) : Package 'maigesPack' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'maigesPack' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (maigesPack)
maigesPack.Rcheck/maigesPack-Ex.timings
| name | user | system | elapsed | |
| MI | 0 | 0 | 0 | |
| activeMod | 1.36 | 0.91 | 2.31 | |
| activeModScoreHTML | 0.69 | 0.33 | 1.11 | |
| activeNet | 2.06 | 0.33 | 2.50 | |
| activeNetScoreHTML | 2.19 | 0.36 | 2.59 | |
| addGeneGrps | 0 | 0 | 0 | |
| addPaths | 0 | 0 | 0 | |
| bootstrapCor | 0.04 | 0.00 | 0.05 | |
| bootstrapMI | 0.13 | 0.01 | 0.14 | |
| bootstrapT | 0 | 0 | 0 | |
| boxplot-methods | 2.65 | 2.41 | 5.11 | |
| bracketMethods | 0.11 | 0.03 | 0.14 | |
| calcA | 0.19 | 0.08 | 0.27 | |
| calcW | 0.20 | 0.09 | 0.29 | |
| classifyKNN | 0.22 | 0.61 | 0.88 | |
| classifyKNNsc | 0.21 | 0.63 | 0.84 | |
| classifyLDA | 0.46 | 0.71 | 1.21 | |
| classifyLDAsc | 0.91 | 0.66 | 1.65 | |
| classifySVM | 0.30 | 0.68 | 1.00 | |
| classifySVMsc | 0.53 | 0.66 | 1.22 | |
| coerce-methods | 0.08 | 0.05 | 0.12 | |
| compCorr | 0 | 0 | 0 | |
| createMaigesRaw | 0.14 | 0.34 | 0.50 | |
| deGenes2by2BootT | 0.26 | 0.34 | 0.63 | |
| deGenes2by2Ttest | 0.14 | 0.35 | 0.48 | |
| deGenes2by2Wilcox | 0.11 | 0.36 | 0.47 | |
| deGenesANOVA | 0.11 | 0.67 | 0.89 | |
| designANOVA | 0.09 | 0.34 | 0.43 | |
| dim-methods | 0.05 | 0.02 | 0.07 | |
| getLabels | 0.05 | 0.03 | 0.07 | |
| hierM | 0.79 | 0.05 | 0.85 | |
| hierMde | 1.44 | 0.83 | 2.27 | |
| image-methods | 1.04 | 0.89 | 1.98 | |
| kmeansM | 0.94 | 0.06 | 1.00 | |
| kmeansMde | 0.25 | 0.39 | 0.64 | |
| loadData | 0 | 0 | 0 | |
| normLoc | 0.59 | 0.83 | 1.47 | |
| normOLIN | 0.05 | 0.00 | 0.05 | |
| normRepLoess | 0.29 | 0.00 | 0.29 | |
| normScaleLimma | 6.99 | 3.84 | 10.97 | |
| normScaleMarray | 1.29 | 1.28 | 2.59 | |
| plot-methods | 4.35 | 4.60 | 9.24 | |
| plotGenePair | 0.12 | 0.65 | 0.87 | |
| print-methods | 0.13 | 0.02 | 0.14 | |
| relNet2TGF | 0.19 | 0.70 | 0.91 | |
| relNetworkB | 1.43 | 1.42 | 2.91 | |
| relNetworkM | 0.03 | 0.80 | 0.83 | |
| robustCorr | 0 | 0 | 0 | |
| selSpots | 0.30 | 1.36 | 1.78 | |
| show-methods | 0.14 | 0.01 | 0.15 | |
| somM | 1.22 | 0.05 | 1.30 | |
| somMde | 0.30 | 0.75 | 1.06 | |
| summarizeReplicates | 1.56 | 1.47 | 3.08 | |
| summary-methods | 0.09 | 0.00 | 0.11 | |
| tableClass | 0.36 | 0.77 | 1.12 | |
| tablesDE | 3.44 | 2.79 | 6.35 | |