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This page was generated on 2016-04-23 10:18:29 -0700 (Sat, 23 Apr 2016).
| Package 531/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
InSilico DB
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: inSilicoMerging |
| Version: 1.14.1 |
| Command: rm -rf inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && mkdir inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=inSilicoMerging.buildbin-libdir inSilicoMerging_1.14.1.tar.gz >inSilicoMerging.Rcheck\00install.out 2>&1 && cp inSilicoMerging.Rcheck\00install.out inSilicoMerging-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=inSilicoMerging.buildbin-libdir --install="check:inSilicoMerging-install.out" --force-multiarch --no-vignettes --timings inSilicoMerging_1.14.1.tar.gz |
| StartedAt: 2016-04-23 03:49:25 -0700 (Sat, 23 Apr 2016) |
| EndedAt: 2016-04-23 03:50:44 -0700 (Sat, 23 Apr 2016) |
| EllapsedTime: 79.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: inSilicoMerging.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### rm -rf inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && mkdir inSilicoMerging.buildbin-libdir inSilicoMerging.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=inSilicoMerging.buildbin-libdir inSilicoMerging_1.14.1.tar.gz >inSilicoMerging.Rcheck\00install.out 2>&1 && cp inSilicoMerging.Rcheck\00install.out inSilicoMerging-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=inSilicoMerging.buildbin-libdir --install="check:inSilicoMerging-install.out" --force-multiarch --no-vignettes --timings inSilicoMerging_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'inSilicoMerging/DESCRIPTION' ... OK
* this is package 'inSilicoMerging' version '1.14.1'
* 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 whether package 'inSilicoMerging' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'Biobase'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
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
commonGenes : <anonymous>: no visible global function definition for
'exprs'
geneBMCESet: no visible global function definition for 'exprs<-'
geneBMCESet: no visible global function definition for 'exprs'
geneNormESet: no visible global function definition for 'exprs<-'
geneNormESet: no visible global function definition for 'exprs'
identify_common_genes: no visible global function definition for
'exprs'
makeColorMap: no visible global function definition for 'pData'
makeColorVec: no visible global function definition for 'pData'
matchExprsPheno: no visible global function definition for 'exprs'
matchExprsPheno: no visible global function definition for 'pData<-'
matchExprsPheno: no visible global function definition for 'pData'
mergeCOMBAT: no visible global function definition for 'pData'
mergeCOMBAT: no visible global function definition for 'exprs'
mergeCOMBAT: no visible global function definition for 'exprs<-'
mergeNONE: no visible global function definition for 'annotation'
mergeNONE: no visible global function definition for 'exprs'
mergeNONE: no visible global function definition for 'exprs<-'
mergeNONE: no visible global function definition for 'pData<-'
mergeNONE: no visible global function definition for 'fData<-'
mergeNONE: no visible global function definition for 'annotation<-'
plotGeneWiseBoxPlot: no visible global function definition for 'exprs'
plotGeneWiseBoxPlot: no visible global function definition for 'pData'
plotMDS: no visible global function definition for 'exprs'
plotMDS: no visible global function definition for 'pData'
plotRLE: no visible global function definition for 'exprs'
plotRLE: no visible global function definition for 'rowMedians'
xpn: no visible global function definition for 'exprs'
xpn: no visible global function definition for 'exprs<-'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'inSilicoMerging-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: merge
> ### Title: General method to merge different ExpressionSets
> ### Aliases: merge
>
> ### ** Examples
>
>
> # retrieve two datasets:
> library(inSilicoDb);
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
INSILICODB: Welcome RPackage Tester
[1] 5296
> eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="GENE");
INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Error: Stopped because of previous errors
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'inSilicoMerging-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: merge
> ### Title: General method to merge different ExpressionSets
> ### Aliases: merge
>
> ### ** Examples
>
>
> # retrieve two datasets:
> library(inSilicoDb);
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
INSILICODB: Welcome RPackage Tester
[1] 5296
> eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="GENE");
INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Error: Stopped because of previous errors
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'inSilicoMerging_unit_tests.R' [6s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "inSilicoMerging_unit_tests.R" "inSilicoMerging_unit_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/inSilicoMerging_unit_tests.R' failed.
Last 13 lines of output:
inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors
Test files with failing tests
test_inSilicoMerging.R
test.compare_null_bmc_merge
Error in BiocGenerics:::testPackage("inSilicoMerging") :
unit tests failed for package inSilicoMerging
Calls: <Anonymous> -> <Anonymous>
Execution halted
** running tests for arch 'x64' ...
Running 'inSilicoMerging_unit_tests.R' [6s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "inSilicoMerging_unit_tests.R" "inSilicoMerging_unit_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/inSilicoMerging_unit_tests.R' failed.
Last 13 lines of output:
inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors
Test files with failing tests
test_inSilicoMerging.R
test.compare_null_bmc_merge
Error in BiocGenerics:::testPackage("inSilicoMerging") :
unit tests failed for package inSilicoMerging
Calls: <Anonymous> -> <Anonymous>
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: 4 ERRORs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck/00check.log'
for details.
inSilicoMerging_unit_tests.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 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.
> require("inSilicoMerging") || stop("unable to load inSilicoMerging package")
Loading required package: inSilicoMerging
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'inSilicoMerging'
The following object is masked from 'package:base':
merge
[1] TRUE
> inSilicoMerging:::.test()
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
INSILICODB: Welcome RPackage Tester
INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Timing stopped at: 0.47 0.01 3.87
Error : Stopped because of previous errors
RUNIT TEST PROTOCOL -- Sat Apr 23 03:50:31 2016
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors
Test files with failing tests
test_inSilicoMerging.R
test.compare_null_bmc_merge
Error in BiocGenerics:::testPackage("inSilicoMerging") :
unit tests failed for package inSilicoMerging
Calls: <Anonymous> -> <Anonymous>
Execution halted
inSilicoMerging_unit_tests.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 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.
> require("inSilicoMerging") || stop("unable to load inSilicoMerging package")
Loading required package: inSilicoMerging
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'inSilicoMerging'
The following object is masked from 'package:base':
merge
[1] TRUE
> inSilicoMerging:::.test()
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
INSILICODB: Welcome RPackage Tester
INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Timing stopped at: 0.45 0.03 3.82
Error : Stopped because of previous errors
RUNIT TEST PROTOCOL -- Sat Apr 23 03:50:37 2016
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors
Test files with failing tests
test_inSilicoMerging.R
test.compare_null_bmc_merge
Error in BiocGenerics:::testPackage("inSilicoMerging") :
unit tests failed for package inSilicoMerging
Calls: <Anonymous> -> <Anonymous>
Execution halted
inSilicoMerging.Rcheck/00install.out:
install for i386 * installing *source* package 'inSilicoMerging' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'inSilicoMerging' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'inSilicoMerging' as inSilicoMerging_1.14.1.zip * DONE (inSilicoMerging)
inSilicoMerging.Rcheck/examples_i386/inSilicoMerging-Ex.timings:
| name | user | system | elapsed |
inSilicoMerging.Rcheck/examples_x64/inSilicoMerging-Ex.timings:
| name | user | system | elapsed |