| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:39 -0400 (Sat, 13 Apr 2019).
| Package 1131/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Cristobal Fresno
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: pbcmc |
| Version: 1.10.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pbcmc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pbcmc_1.10.1.tar.gz |
| StartedAt: 2019-04-13 04:25:48 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:33:14 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 445.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pbcmc.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pbcmc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pbcmc_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pbcmc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pbcmc' version '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'pbcmc' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck/00install.out' for details.
* 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 ... OK
* 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 or elapsed time > 5s
user system elapsed
PAM50-class 2.21 0.16 15.42
MolecularPermutationClassifierGenerics 0.20 0.01 21.73
PAM50Permutate 0.08 0.06 28.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PAM50-class 3.08 0.10 16.20
MolecularPermutationClassifierGenerics 0.35 0.04 28.11
PAM50Permutate 0.20 0.00 23.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Test files with failing tests
test_pbcmc.R
test_databaseReport
test_subjectReport
Error in BiocGenerics:::testPackage("pbcmc") :
unit tests failed for package pbcmc
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Test files with failing tests
test_pbcmc.R
test_databaseReport
test_subjectReport
Error in BiocGenerics:::testPackage("pbcmc") :
unit tests failed for package pbcmc
Execution halted
* 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 ERRORs, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck/00check.log'
for details.
pbcmc.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pbcmc_1.10.1.tar.gz && rm -rf pbcmc.buildbin-libdir && mkdir pbcmc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pbcmc.buildbin-libdir pbcmc_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pbcmc_1.10.1.zip && rm pbcmc_1.10.1.tar.gz pbcmc_1.10.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 555k 100 555k 0 0 11.3M 0 --:--:-- --:--:-- --:--:-- 12.3M
install for i386
* installing *source* package 'pbcmc' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
** help
*** installing help indices
converting help for package 'pbcmc'
finding HTML links ... done
MolecularPermutationClassifier-class html
MolecularPermutationClassifierConstructor
html
MolecularPermutationClassifierGenerics
html
MolecularPermutationClassifierGetseters
html
MolecularPermutationClassifierShow html
PAM50-class html
PAM50Classify html
PAM50Constructor html
finding level-2 HTML links ... done
PAM50Filtrate html
PAM50Permutate html
PAM50SubjectReport html
PAM50Subtype html
pbcmcData html
pbcmcPackage html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
version 3.9
In R CMD INSTALL
install for x64
* installing *source* package 'pbcmc' ...
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
version 3.9
* MD5 sums
packaged installation of 'pbcmc' as pbcmc_1.10.1.zip
* DONE (pbcmc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pbcmc' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
pbcmc.Rcheck/tests_i386/runTests.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("pbcmc")
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
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 object is masked from 'package:limma':
plotMA
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Loading required namespace: breastCancerNKI
Timing stopped at: 1.67 0.34 2.01
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
In addition: Warning message:
Package 'pbcmc' is deprecated and will be removed from Bioconductor
version 3.9
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Timing stopped at: 1.41 0.05 1.46
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
RUNIT TEST PROTOCOL -- Sat Apr 13 04:32:27 2019
***********************************************
Number of test functions: 14
Number of errors: 0
Number of failures: 2
1 Test Suite :
pbcmc RUnit Tests - 14 test functions, 0 errors, 2 failures
FAILURE in test_databaseReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Test files with failing tests
test_pbcmc.R
test_databaseReport
test_subjectReport
Error in BiocGenerics:::testPackage("pbcmc") :
unit tests failed for package pbcmc
Execution halted
|
pbcmc.Rcheck/tests_x64/runTests.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("pbcmc")
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
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 object is masked from 'package:limma':
plotMA
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Loading required namespace: breastCancerNKI
Timing stopped at: 1.36 0.03 1.39
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
In addition: Warning message:
Package 'pbcmc' is deprecated and will be removed from Bioconductor
version 3.9
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Timing stopped at: 1.15 0.03 1.19
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
RUNIT TEST PROTOCOL -- Sat Apr 13 04:33:09 2019
***********************************************
Number of test functions: 14
Number of errors: 0
Number of failures: 2
1 Test Suite :
pbcmc RUnit Tests - 14 test functions, 0 errors, 2 failures
FAILURE in test_databaseReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") :
Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
Test files with failing tests
test_pbcmc.R
test_databaseReport
test_subjectReport
Error in BiocGenerics:::testPackage("pbcmc") :
unit tests failed for package pbcmc
Execution halted
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pbcmc.Rcheck/examples_i386/pbcmc-Ex.timings
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pbcmc.Rcheck/examples_x64/pbcmc-Ex.timings
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