Multiple platform build/check report for BioC 3.15 - CHECK results for maigesPack on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
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*

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings maigesPack_1.60.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/maigesPack.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.60.0’
* 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
normScaleLimma 5.027   0.52   5.549
* 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-3.15-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL maigesPack
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘maigesPack’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Minfo.c -o Minfo.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bootstrapT.c -o bootstrapT.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c robustCorr.c -o robustCorr.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c stats.c -o stats.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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)

Tests output

Example timings

name	user	system	elapsed
MI	0.003	0.000	0.003
activeMod	1.076	0.020	1.095
activeModScoreHTML	0.473	0.004	0.477
activeNet	2.309	0.028	2.339
activeNetScoreHTML	2.201	0.003	2.205
addGeneGrps	0.000	0.000	0.001
addPaths	0	0	0
bootstrapCor	0.027	0.000	0.027
bootstrapMI	0.135	0.000	0.135
bootstrapT	0.002	0.000	0.002
boxplot-methods	2.265	0.136	2.401
bracketMethods	0.113	0.023	0.137
calcA	0.137	0.285	0.421
calcW	0.141	0.283	0.425
classifyKNN	0.157	0.005	0.162
classifyKNNsc	0.223	0.000	0.223
classifyLDA	0.465	0.012	0.477
classifyLDAsc	0.810	0.004	0.814
classifySVM	0.324	0.004	0.327
classifySVMsc	0.524	0.008	0.531
coerce-methods	0.071	0.048	0.119
compCorr	0.001	0.000	0.001
createMaigesRaw	0.151	0.004	0.155
deGenes2by2BootT	0.282	0.004	0.285
deGenes2by2Ttest	0.149	0.000	0.149
deGenes2by2Wilcox	0.148	0.003	0.152
deGenesANOVA	0.110	0.007	0.118
designANOVA	0.093	0.001	0.094
dim-methods	0.063	0.004	0.067
getLabels	0.063	0.016	0.079
hierM	0.877	0.012	0.796
hierMde	1.273	0.032	1.304
image-methods	0.934	0.012	0.946
kmeansM	0.955	0.020	0.936
kmeansMde	0.282	0.008	0.289
loadData	0.000	0.000	0.001
normLoc	0.845	0.008	0.853
normOLIN	0.060	0.004	0.064
normRepLoess	0.062	0.000	0.062
normScaleLimma	5.027	0.520	5.549
normScaleMarray	1.107	0.112	1.219
plot-methods	4.763	0.160	4.901
plotGenePair	0.095	0.003	0.099
print-methods	0.115	0.019	0.135
relNet2TGF	0.096	0.016	0.113
relNetworkB	1.203	0.056	1.259
relNetworkM	0.104	0.004	0.108
robustCorr	0.001	0.000	0.001
selSpots	0.167	0.012	0.178
show-methods	0.112	0.016	0.127
somM	0.939	0.044	0.964
somMde	0.335	0.016	0.353
summarizeReplicates	0.967	0.012	0.979
summary-methods	0.083	0.032	0.114
tableClass	0.418	0.028	0.445
tablesDE	3.621	0.124	3.748

CHECK results for maigesPack on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings