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	4.2.2 (2022-10-31) -- "Innocent and Trusting"	4511
palomino4	Windows Server 2022 Datacenter	x64	4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting"	4289
lconway	macOS 12.5.1 Monterey	x86_64	4.2.2 (2022-10-31) -- "Innocent and Trusting"	4318
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/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 4.2.2 (2022-10-31)
* 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 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 4.994  0.636   5.631
* 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/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/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	0.001	0.003
activeMod	1.055	0.007	1.064
activeModScoreHTML	0.494	0.000	0.493
activeNet	2.429	0.015	2.445
activeNetScoreHTML	2.356	0.008	2.364
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.028	0.000	0.027
bootstrapMI	0.133	0.000	0.133
bootstrapT	0.002	0.000	0.003
boxplot-methods	2.130	0.147	2.278
bracketMethods	0.131	0.004	0.135
calcA	0.119	0.052	0.170
calcW	0.134	0.036	0.169
classifyKNN	0.157	0.008	0.164
classifyKNNsc	0.235	0.000	0.236
classifyLDA	0.539	0.004	0.544
classifyLDAsc	0.852	0.000	0.852
classifySVM	0.365	0.000	0.366
classifySVMsc	0.520	0.007	0.528
coerce-methods	0.081	0.012	0.094
compCorr	0	0	0
createMaigesRaw	0.158	0.000	0.157
deGenes2by2BootT	0.297	0.000	0.297
deGenes2by2Ttest	0.158	0.004	0.162
deGenes2by2Wilcox	0.174	0.005	0.177
deGenesANOVA	0.118	0.007	0.126
designANOVA	0.089	0.004	0.093
dim-methods	0.064	0.003	0.068
getLabels	0.062	0.004	0.066
hierM	0.909	0.000	0.793
hierMde	1.222	0.044	1.266
image-methods	0.989	0.008	0.996
kmeansM	0.981	0.000	0.958
kmeansMde	0.242	0.004	0.245
loadData	0	0	0
normLoc	0.910	0.012	0.922
normOLIN	0.062	0.000	0.061
normRepLoess	0.062	0.000	0.061
normScaleLimma	4.994	0.636	5.631
normScaleMarray	1.238	0.076	1.314
plot-methods	4.769	0.130	4.883
plotGenePair	0.092	0.004	0.097
print-methods	0.113	0.000	0.114
relNet2TGF	0.112	0.000	0.112
relNetworkB	1.218	0.016	1.233
relNetworkM	0.082	0.008	0.090
robustCorr	0.001	0.000	0.000
selSpots	0.152	0.016	0.168
show-methods	0.125	0.004	0.128
somM	0.953	0.012	0.926
somMde	0.262	0.032	0.292
summarizeReplicates	0.979	0.012	0.991
summary-methods	0.106	0.000	0.106
tableClass	0.415	0.016	0.430
tablesDE	4.036	0.152	4.188

CHECK results for maigesPack on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings