Multiple platform build/check report for BioC 3.16 - CHECK results for maigesPack on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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-3.16-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings maigesPack_1.62.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/maigesPack.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.62.0’
* 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 loading without being on the library search path ... 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 4.743  0.288    5.03
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL maigesPack
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘maigesPack’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Minfo.c -o Minfo.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bootstrapT.c -o bootstrapT.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c robustCorr.c -o robustCorr.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c stats.c -o stats.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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)

Tests output

Example timings

name	user	system	elapsed
MI	0.002	0.000	0.003
activeMod	1.023	0.024	1.046
activeModScoreHTML	0.483	0.004	0.487
activeNet	2.306	0.016	2.321
activeNetScoreHTML	2.257	0.000	2.257
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.027	0.000	0.026
bootstrapMI	0.166	0.000	0.165
bootstrapT	0.003	0.000	0.004
boxplot-methods	2.339	0.372	2.711
bracketMethods	0.130	0.012	0.142
calcA	0.112	0.060	0.172
calcW	0.111	0.064	0.175
classifyKNN	0.155	0.004	0.159
classifyKNNsc	0.218	0.008	0.227
classifyLDA	0.509	0.000	0.509
classifyLDAsc	0.795	0.004	0.799
classifySVM	0.321	0.003	0.325
classifySVMsc	0.599	0.000	0.599
coerce-methods	0.091	0.000	0.091
compCorr	0	0	0
createMaigesRaw	0.153	0.000	0.153
deGenes2by2BootT	0.288	0.000	0.288
deGenes2by2Ttest	0.15	0.00	0.15
deGenes2by2Wilcox	0.145	0.004	0.149
deGenesANOVA	0.117	0.000	0.117
designANOVA	0.078	0.008	0.086
dim-methods	0.058	0.008	0.065
getLabels	0.067	0.000	0.067
hierM	0.898	0.008	0.804
hierMde	1.247	0.040	1.287
image-methods	0.991	0.012	1.002
kmeansM	0.956	0.000	0.918
kmeansMde	0.232	0.000	0.231
loadData	0.001	0.000	0.000
normLoc	0.835	0.008	0.844
normOLIN	0.06	0.00	0.06
normRepLoess	0.055	0.004	0.060
normScaleLimma	4.743	0.288	5.030
normScaleMarray	1.208	0.044	1.251
plot-methods	4.592	0.069	4.639
plotGenePair	0.087	0.004	0.092
print-methods	0.101	0.004	0.106
relNet2TGF	0.086	0.016	0.102
relNetworkB	1.192	0.044	1.236
relNetworkM	0.078	0.004	0.081
robustCorr	0.001	0.000	0.001
selSpots	0.162	0.008	0.170
show-methods	0.103	0.012	0.115
somM	0.923	0.048	0.931
somMde	0.264	0.000	0.262
summarizeReplicates	0.957	0.012	0.969
summary-methods	0.108	0.000	0.108
tableClass	0.400	0.012	0.411
tablesDE	3.672	0.252	3.924

CHECK results for maigesPack on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings