Xuejun Liu
| Snapshot Date: 2025-04-28 17:48 -0400 (Mon, 28 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/puma |
| git_branch: RELEASE_3_21 |
| git_last_commit: 189a758 |
| git_last_commit_date: 2025-04-15 09:40:26 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-05-01 11:42 -0400 (Thu, 01 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4553 |
| 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 1647/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| puma 3.50.0 (landing page) Xuejun Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the puma package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/puma.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: puma |
| Version: 3.50.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:puma.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings puma_3.50.0.tar.gz |
| StartedAt: 2025-04-29 11:35:41 -0400 (Tue, 29 Apr 2025) |
| EndedAt: 2025-04-29 11:46:48 -0400 (Tue, 29 Apr 2025) |
| EllapsedTime: 666.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: puma.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:puma.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings puma_3.50.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/puma.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘3.50.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘puma’ can be installed ... WARNING
Found the following significant warnings:
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/puma.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘oligoClasses’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘ROCR’ ‘limma’ ‘pumadata’ ‘snow’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
‘affy:::mm’ ‘affy:::pm’ ‘affy:::probeNames’ ‘oligo:::mm’ ‘oligo:::pm’
‘oligo:::probeNames’ ‘oligo:::rma’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMmmgmos: no visible binding for global variable ‘median’
PMmmgmos: no visible global function definition for ‘description’
calcAUC: no visible global function definition for ‘prediction’
calcAUC: no visible global function definition for ‘performance’
calculateLimma: no visible global function definition for ‘lmFit’
calculateLimma: no visible global function definition for
‘contrasts.fit’
calculateLimma: no visible global function definition for ‘eBayes’
calculateTtest : <anonymous>: no visible global function definition for
‘t.test’
clusterApplyLBDots : submit: no visible global function definition for
‘sendCall’
clusterApplyLBDots: no visible global function definition for
‘recvOneResult’
clusterNormE: no visible global function definition for ‘var’
clusterNormVar: no visible global function definition for ‘var’
compareLimmapumaDE: no visible global function definition for ‘pdf’
compareLimmapumaDE: no visible global function definition for ‘dev.off’
compareLimmapumaDE: no visible global function definition for ‘par’
compareLimmapumaDE: no visible global function definition for
‘vennDiagram’
createDesignMatrix: no visible global function definition for
‘model.matrix’
erfc: no visible global function definition for ‘pnorm’
gmhta: no visible global function definition for ‘clusterEvalQ’
gmhta: no visible global function definition for ‘data’
gmhta: no visible global function definition for ‘clusterApplyLB’
gmhta: no visible global function definition for ‘stopCluster’
gmhta: no visible binding for global variable ‘median’
gmoExon: no visible global function definition for ‘clusterEvalQ’
gmoExon: no visible global function definition for ‘data’
gmoExon: no visible global function definition for ‘clusterApplyLB’
gmoExon: no visible global function definition for ‘stopCluster’
gmoExon: no visible binding for global variable ‘median’
igmoExon: no visible global function definition for ‘clusterEvalQ’
igmoExon: no visible global function definition for ‘read.table’
igmoExon: no visible global function definition for ‘data’
igmoExon: no visible global function definition for ‘clusterApplyLB’
igmoExon: no visible global function definition for ‘stopCluster’
igmoExon: no visible binding for global variable ‘median’
just.mgmos: no visible binding for global variable ‘median’
just.mmgmos: no visible binding for global variable ‘median’
legend2: no visible global function definition for ‘par’
legend2: no visible global function definition for ‘xy.coords’
legend2 : rect2: no visible global function definition for ‘rect’
legend2 : segments2: no visible global function definition for
‘segments’
legend2 : points2: no visible global function definition for ‘points’
legend2 : text2: no visible global function definition for ‘text’
legend2: no visible global function definition for ‘strwidth’
legend2: no visible global function definition for ‘xinch’
legend2: no visible global function definition for ‘yinch’
legend2: no visible global function definition for ‘strheight’
matrixDistance: no visible global function definition for ‘dist’
mgmos: no visible binding for global variable ‘median’
mmgmos: no visible binding for global variable ‘median’
plot.pumaPCARes: no visible global function definition for ‘text’
plot.pumaPCARes: no visible global function definition for ‘legend’
plotErrorBars: no visible global function definition for ‘qnorm’
plotErrorBars: no visible global function definition for ‘par’
plotErrorBars: no visible global function definition for ‘even’
plotErrorBars: no visible global function definition for ‘odd’
plotErrorBars: no visible global function definition for ‘arrows’
plotErrorBars: no visible global function definition for ‘points’
plotErrorBars: no visible global function definition for ‘axis’
plotErrorBars: no visible global function definition for ‘title’
plotHistTwoClasses: no visible global function definition for ‘axis’
plotHistTwoClasses: no visible global function definition for ‘box’
plotROC: no visible global function definition for ‘prediction’
plotROC: no visible global function definition for ‘performance’
plotWhiskers: no visible global function definition for ‘segments’
plotWhiskers: no visible global function definition for ‘qnorm’
plotWhiskers: no visible global function definition for ‘points’
plotWhiskers: no visible global function definition for ‘abline’
pumaClust: no visible global function definition for ‘read.csv’
pumaClust: no visible global function definition for ‘kmeans’
pumaClust: no visible global function definition for ‘cov’
pumaClustii: no visible global function definition for ‘read.csv’
pumaClustii: no visible global function definition for ‘cov’
pumaComb: no visible global function definition for ‘getMPIcluster’
pumaComb: no visible global function definition for ‘makeCluster’
pumaComb: no visible global function definition for ‘clusterEvalQ’
pumaComb: no visible global function definition for ‘clusterApplyLB’
pumaCombImproved: no visible global function definition for
‘getMPIcluster’
pumaCombImproved: no visible global function definition for
‘makeCluster’
pumaCombImproved: no visible global function definition for
‘clusterEvalQ’
pumaCombImproved: no visible global function definition for
‘clusterApplyLB’
pumaFull: no visible global function definition for ‘pdf’
pumaFull: no visible global function definition for ‘par’
pumaFull: no visible global function definition for ‘prcomp’
pumaFull: no visible global function definition for ‘dev.off’
pumaNormalize: no visible binding for global variable ‘median’
pumaPCA: no visible global function definition for ‘prcomp’
pumaPCA: no visible global function definition for ‘rnorm’
pumaPCA: no visible global function definition for ‘optimise’
pumaPCA: no visible global function definition for ‘optim’
pumaPCA: no visible global function definition for ‘par’
pumaPCARemoveRedundancy: no visible global function definition for
‘dist’
write.reslts,DEResult: no visible global function definition for
‘write.table’
write.reslts,ExpressionSet: no visible global function definition for
‘write.table’
write.reslts,exprReslt: no visible global function definition for
‘write.table’
write.reslts,pumaPCARes: no visible global function definition for
‘write.table’
Undefined global functions or variables:
abline arrows axis box clusterApplyLB clusterEvalQ contrasts.fit cov
data description dev.off dist eBayes even getMPIcluster kmeans legend
lmFit makeCluster median model.matrix odd optim optimise par pdf
performance pnorm points prcomp prediction qnorm read.csv read.table
rect recvOneResult rnorm segments sendCall stopCluster strheight
strwidth t.test text title var vennDiagram write.table xinch
xy.coords yinch
Consider adding
importFrom("grDevices", "dev.off", "pdf", "xy.coords")
importFrom("graphics", "abline", "arrows", "axis", "box", "legend",
"par", "points", "rect", "segments", "strheight",
"strwidth", "text", "title", "xinch", "yinch")
importFrom("stats", "cov", "dist", "kmeans", "median", "model.matrix",
"optim", "optimise", "pnorm", "prcomp", "qnorm", "rnorm",
"t.test", "var")
importFrom("utils", "data", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) DEResult-class.Rd:92: Escaped LaTeX specials: \_
checkRd: (-1) DEResult-class.Rd:93: Escaped LaTeX specials: \_
checkRd: (-1) PMmmgmos.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) PMmmgmos.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) createContrastMatrix.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) exprReslt-class.Rd:100: Escaped LaTeX specials: \_
checkRd: (-1) exprReslt-class.Rd:101: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) exprReslt-class.Rd:102: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) gmhta.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) gmoExon.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hcomb.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) hcomb.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) igmoExon.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) justmgMOS.Rd:41: Escaped LaTeX specials: \_ \_
checkRd: (-1) justmmgMOS.Rd:41: Escaped LaTeX specials: \_ \_
checkRd: (-1) legend2.Rd:134: Escaped LaTeX specials: \&
checkRd: (-1) mgmos.Rd:25: Escaped LaTeX specials: \_ \_
checkRd: (-1) mgmos.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) mmgmos.Rd:26: Escaped LaTeX specials: \_ \_
checkRd: (-1) mmgmos.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) mmgmos.Rd:38: Escaped LaTeX specials: \_
checkRd: (-1) pumaFull.Rd:23: Escaped LaTeX specials: \_ \_
checkRd: (-1) pumaFull.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) pumaFull.Rd:25: Escaped LaTeX specials: \_ \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'bcomb.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'calculateFC.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'calculateLimma.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'calculateTtest.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'clusterApplyLBDots.Rd':
‘[snow:snow-cluster]{clusterApplyLB}’
Non-topic package-anchored link(s) in Rd file 'compareLimmapumaDE.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'createContrastMatrix.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
Non-topic package-anchored link(s) in Rd file 'createDesignMatrix.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
Non-topic package-anchored link(s) in Rd file 'create_eset_r.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'eset_mmgmos.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'exprReslt-class.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'justmgMOS.Rd':
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
‘[Biobase:class.MIAME]{MIAME}’
Non-topic package-anchored link(s) in Rd file 'justmmgMOS.Rd':
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
‘[Biobase:class.MIAME]{MIAME}’
Non-topic package-anchored link(s) in Rd file 'numOfFactorsToUse.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'plotErrorBars.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'plotWhiskers.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'pumaClustii.Rd':
‘[puma]{pumaclust}’
Non-topic package-anchored link(s) in Rd file 'pumaComb.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
‘[snow:snow-startstop]{makeCluster}’
Non-topic package-anchored link(s) in Rd file 'pumaCombImproved.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
‘[snow:snow-startstop]{makeCluster}’
Non-topic package-anchored link(s) in Rd file 'pumaDE.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'pumaNormalize.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'pumaPCA.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'pumaclust.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'removeUninformativeFactors.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
puma-package 77.992 4.256 88.946
pumaDE 50.618 2.739 54.870
pumaCombImproved 31.877 2.318 35.792
pumaComb 19.252 0.662 20.947
plot-methods 12.526 0.586 13.680
pumaPCA 11.949 0.230 12.497
pumaclust 6.196 0.040 6.300
* 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: 1 WARNING, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/puma.Rcheck/00check.log’
for details.
puma.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL puma
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘puma’ ...
** this is package ‘puma’ version ‘3.50.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PMmultimgmos.c -o PMmultimgmos.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cregistration.c -o cregistration.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c donlp2.c -o donlp2.o
donlp2.c:471:33: warning: variable 'infiny' set but not used [-Wunused-but-set-variable]
static DDOUBLE tol1,term, infiny;
^
donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive
^
donlp2.c:2079:44: warning: variable 'iumin' set but not used [-Wunused-but-set-variable]
static DDOUBLE delsig,delx,sum,term, iumin;
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gme.c -o gme.o
gme.c:266:9: warning: variable 'fstart' set but not used [-Wunused-but-set-variable]
double fstart;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ipplr_c.c -o ipplr_c.o
ipplr_c.c:255:118: warning: '&&' within '||' [-Wlogical-op-parentheses]
while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
ipplr_c.c:255:118: note: place parentheses around the '&&' expression to silence this warning
while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000))
^
( )
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multimgmos.c -o multimgmos.o
multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces]
double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4;
^~~
{ }
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c newx.c -o newx.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pplr_c.c -o pplr_c.o
pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable]
double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pumaclust_c.c -o pumaclust_c.o
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
while (foptold-fopt > abs(in_param.eps*fopt))
^
pumaclust_c.c:181:24: note: use function 'fabs' instead
while (foptold-fopt > abs(in_param.eps*fopt))
^~~
fabs
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pumaclustii_c.c -o pumaclustii_c.o
pumaclustii_c.c:255:42: warning: variable 'temp2' set but not used [-Wunused-but-set-variable]
double *exprs=NULL, *vars=NULL, temp, *temp2, temp3, **t3=NULL, *t4=NULL;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c user_eval.c -o user_eval.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-puma/00new/puma/libs
** R
** data
** demo
** inst
** 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 (puma)
puma.Rcheck/puma-Ex.timings
| name | user | system | elapsed | |
| DEResult-class | 0.004 | 0.002 | 0.005 | |
| PMmmgmos | 0.001 | 0.001 | 0.001 | |
| bcomb | 0 | 0 | 0 | |
| calcAUC | 0.000 | 0.001 | 0.001 | |
| calculateFC | 0.000 | 0.001 | 0.001 | |
| calculateLimma | 0.000 | 0.000 | 0.001 | |
| calculateTtest | 0 | 0 | 0 | |
| clusterNormE | 0.001 | 0.001 | 0.001 | |
| clusterNormVar | 0.000 | 0.001 | 0.001 | |
| createContrastMatrix | 0.046 | 0.004 | 0.050 | |
| createDesignMatrix | 0.065 | 0.005 | 0.070 | |
| erfc | 0.000 | 0.001 | 0.001 | |
| exprReslt-class | 0.001 | 0.001 | 0.002 | |
| gmhta | 0.000 | 0.001 | 0.001 | |
| gmoExon | 0.000 | 0.001 | 0.001 | |
| hcomb | 0.001 | 0.000 | 0.001 | |
| igmoExon | 0.000 | 0.001 | 0.001 | |
| legend2 | 0.001 | 0.001 | 0.002 | |
| license.puma | 0.002 | 0.002 | 0.003 | |
| matrixDistance | 0.001 | 0.001 | 0.001 | |
| mgmos | 0.000 | 0.000 | 0.001 | |
| mmgmos | 0.000 | 0.000 | 0.001 | |
| normalisation.gs | 0.001 | 0.000 | 0.000 | |
| numFP | 0.001 | 0.001 | 0.001 | |
| numOfFactorsToUse | 0.000 | 0.001 | 0.001 | |
| numTP | 0.001 | 0.000 | 0.001 | |
| orig_pplr | 0.000 | 0.000 | 0.001 | |
| plot-methods | 12.526 | 0.586 | 13.680 | |
| plotErrorBars | 0.384 | 0.015 | 0.422 | |
| plotHistTwoClasses | 0.017 | 0.002 | 0.019 | |
| plotROC | 0.001 | 0.001 | 0.002 | |
| pplr | 0.363 | 0.048 | 0.430 | |
| puma-package | 77.992 | 4.256 | 88.946 | |
| pumaClustii | 4.518 | 0.040 | 4.879 | |
| pumaComb | 19.252 | 0.662 | 20.947 | |
| pumaCombImproved | 31.877 | 2.318 | 35.792 | |
| pumaDE | 50.618 | 2.739 | 54.870 | |
| pumaFull | 0.000 | 0.001 | 0.001 | |
| pumaNormalize | 0.356 | 0.018 | 0.441 | |
| pumaPCA | 11.949 | 0.230 | 12.497 | |
| pumaclust | 6.196 | 0.040 | 6.300 | |
| removeUninformativeFactors | 0.066 | 0.001 | 0.067 | |