Hung Nguyen
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/BLMA |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9b4e0e3 |
| git_last_commit_date: 2021-05-19 12:27:28 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the BLMA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BLMA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 200/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BLMA 1.16.0 (landing page) Hung Nguyen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BLMA |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BLMA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BLMA_1.16.0.tar.gz |
| StartedAt: 2021-10-14 20:22:23 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:34:43 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 740.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BLMA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BLMA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BLMA_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BLMA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BLMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BLMA' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'ROntoTools', 'GSA', 'PADOG', 'limma', 'graph', 'parallel',
'Biobase', 'metafor'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'BLMA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addCLT: warning in pnorm(mean(x), 1/2, sqrt(1/(12 * n)), lower = TRUE):
partial argument match of 'lower' to 'lower.tail'
additiveMethod: warning in pnorm(sum(x), n/2, sqrt(n/12), lower =
TRUE): partial argument match of 'lower' to 'lower.tail'
bilevelAnalysisGeneset : <anonymous>: warning in topTable(fit2, adjust
= "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
pCutoff): partial argument match of 'adjust' to 'adjust.method'
bilevelAnalysisPathway : <anonymous>: warning in topTable(fit2, adjust
= "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
pCutoff): partial argument match of 'adjust' to 'adjust.method'
fisherMethod: warning in pchisq(-2 * sum(log(x)), df = 2 * length(x),
lower = FALSE): partial argument match of 'lower' to 'lower.tail'
getStatistics: warning in topTable(fit2, adjust = "fdr", sort.by = "B",
number = Inf): partial argument match of 'adjust' to 'adjust.method'
intraAnalysisGene : <anonymous>: warning in topTable(fit2, adjust =
"none", sort.by = "none", number = Inf): partial argument match of
'adjust' to 'adjust.method'
intraAnalysisGene: warning in topTable(fit2, adjust = "none", sort.by =
"none", number = Inf): partial argument match of 'adjust' to
'adjust.method'
calculateFC: no visible binding for global variable 'm1i'
calculateFC: no visible binding for global variable 'sd1i'
calculateFC: no visible binding for global variable 'n1i'
calculateFC: no visible binding for global variable 'm2i'
calculateFC: no visible binding for global variable 'sd2i'
calculateFC: no visible binding for global variable 'n2i'
calculateFC: no visible binding for global variable 'yi'
getStatistics: no visible binding for global variable 'd'
hierClustering: no visible binding for global variable 'km'
hierClustering: no visible global function definition for 'clusGap'
hierClustering: no visible global function definition for 'maxSE'
intraAnalysisGene: no visible binding for global variable 'd'
Undefined global functions or variables:
clusGap d km m1i m2i maxSE n1i n2i sd1i sd2i yi
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bilevelAnalysisGeneset 89.31 0.48 89.95
getStatistics 65.32 0.99 66.31
bilevelAnalysisPathway 60.43 0.22 60.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bilevelAnalysisGeneset 83.62 1.78 85.42
getStatistics 83.91 1.00 84.92
bilevelAnalysisPathway 66.05 0.19 66.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/BLMA.Rcheck/00check.log'
for details.
BLMA.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BLMA_1.16.0.tar.gz && rm -rf BLMA.buildbin-libdir && mkdir BLMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BLMA.buildbin-libdir BLMA_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BLMA_1.16.0.zip && rm BLMA_1.16.0.tar.gz BLMA_1.16.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
32 2574k 32 823k 0 0 1621k 0 0:00:01 --:--:-- 0:00:01 1622k
100 2574k 100 2574k 0 0 2306k 0 0:00:01 0:00:01 --:--:-- 2308k
install for i386
* installing *source* package 'BLMA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BLMA'
finding HTML links ... done
GSE17054 html
GSE33223 html
GSE42140 html
GSE57194 html
addCLT html
bilevelAnalysisClassic html
bilevelAnalysisGene html
bilevelAnalysisGeneset html
finding level-2 HTML links ... done
bilevelAnalysisPathway html
fisherMethod html
getStatistics html
intraAnalysisClassic html
intraAnalysisGene html
loadKEGGPathways html
pORACalc html
stoufferMethod html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'BLMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BLMA' as BLMA_1.16.0.zip
* DONE (BLMA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BLMA' successfully unpacked and MD5 sums checked
|
BLMA.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("BLMA")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
The following object is masked from 'package:base':
plot
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading the 'metafor' package (version 3.0-2). For an
introduction to the package please type: help(metafor)
Working on dataset GSE17054, 9 samples
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
RUNIT TEST PROTOCOL -- Thu Oct 14 20:34:03 2021
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
BLMA RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
24.85 0.73 25.57
|
BLMA.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("BLMA")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
The following object is masked from 'package:base':
plot
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading the 'metafor' package (version 3.0-2). For an
introduction to the package please type: help(metafor)
Working on dataset GSE17054, 9 samples
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
RUNIT TEST PROTOCOL -- Thu Oct 14 20:34:28 2021
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
BLMA RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
24.20 0.46 24.65
|
|
BLMA.Rcheck/examples_i386/BLMA-Ex.timings
|
BLMA.Rcheck/examples_x64/BLMA-Ex.timings
|