| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:35:38 -0400 (Tue, 09 Apr 2019).
| Package 1606/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFEA.ChIP 1.3.5 Laura Puente Santamaría
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: TFEA.ChIP |
| Version: 1.3.5 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFEA.ChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.3.5.tar.gz |
| StartedAt: 2019-04-09 06:19:26 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:27:49 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 502.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TFEA.ChIP.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFEA.ChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.3.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TFEA.ChIP.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFEA.ChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFEA.ChIP' version '1.3.5'
* package encoding: UTF-8
* 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 'TFEA.ChIP' 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 ... 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' ... ERROR
Running examples in 'TFEA.ChIP-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GeneID2entrez
> ### Title: Translates gene IDs from Gene Symbol or Ensemble ID to Entrez
> ### ID.
> ### Aliases: GeneID2entrez
>
> ### ** Examples
>
> GeneID2entrez(c('TNMD','DPM1','SCYL3','FGR','CFH','FUCA2','GCLC'))
Done! 7 genes of 7 successfully translated.
[1] "64102" "8813" "57147" "2268" "3075" "2519" "2729"
> GeneID2entrez(c('Mcm6', 'Rpl7', 'Itch' ), mode ="m2m")
Error in GeneID2entrez(c("Mcm6", "Rpl7", "Itch"), mode = "m2m") :
We are having trouble reaching biomaRt.
Please, try again later.
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
contingency_matrix 8.16 0.30 8.45
GSEA_run 7.13 0.34 7.48
GeneID2entrez 1.46 0.03 33.42
* 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:
1 Test Suite :
TFEA.ChIP RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_contingency_matrix: Error in get_chip_index(TFfilter = "EPAS1") :
No ChIP-Seq dataset in the database follows your conditions.
Test files with failing tests
test_TFEA.ChIP.R
test_contingency_matrix
Error in BiocGenerics:::testPackage(pkgname = "TFEA.ChIP") :
unit tests failed for package TFEA.ChIP
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
TFEA.ChIP RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_contingency_matrix: Error in get_chip_index(TFfilter = "EPAS1") :
No ChIP-Seq dataset in the database follows your conditions.
Test files with failing tests
test_TFEA.ChIP.R
test_contingency_matrix
Error in BiocGenerics:::testPackage(pkgname = "TFEA.ChIP") :
unit tests failed for package TFEA.ChIP
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: 3 ERRORs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/TFEA.ChIP.Rcheck/00check.log'
for details.
TFEA.ChIP.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TFEA.ChIP_1.3.5.tar.gz && rm -rf TFEA.ChIP.buildbin-libdir && mkdir TFEA.ChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFEA.ChIP.buildbin-libdir TFEA.ChIP_1.3.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TFEA.ChIP_1.3.5.zip && rm TFEA.ChIP_1.3.5.tar.gz TFEA.ChIP_1.3.5.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
100 3908k 100 3908k 0 0 22.0M 0 --:--:-- --:--:-- --:--:-- 22.8M
install for i386
* installing *source* package 'TFEA.ChIP' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TFEA.ChIP'
finding HTML links ... done
ARNT.metadata html
ARNT.peaks.bed html
CM_list html
DnaseHS_db html
Entrez.gene.IDs html
GR2tfbs_db html
GSEA.result html
GSEA_ESpermutations html
GSEA_EnrichmentScore html
GSEA_run html
GeneID2entrez html
Genes.Upreg html
Mat01 html
MetaData html
Select_genes html
contingency_matrix html
getCMstats html
get_LFC_bar html
get_chip_index html
gr.list html
highlight_TF html
hypoxia html
hypoxia_DESeq html
log2.FC html
makeTFBSmatrix html
plot_CM html
plot_ES html
plot_RES html
preprocessInputData html
rankTFs html
set_user_data html
stat_mat html
tfbs.database html
txt2GR 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 'TFEA.ChIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFEA.ChIP' as TFEA.ChIP_1.3.5.zip
* DONE (TFEA.ChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TFEA.ChIP' successfully unpacked and MD5 sums checked
|
TFEA.ChIP.Rcheck/tests_i386/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(pkgname = "TFEA.ChIP")
Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from the ENCODE project.
To download the full ReMap database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Done! 2 genes of 2 successfully translated.
Done! 1 genes of 1 successfully translated.
Done! 1 genes of 1 successfully translated.
Done! 2 genes of 2 successfully translated.
Timing stopped at: 6.36 0.28 6.64
Error in get_chip_index(TFfilter = "EPAS1") :
No ChIP-Seq dataset in the database follows your conditions.
In addition: Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
Done! 16975 genes of 17527 successfully translated.
Couldn't find Entrez IDs for 552 genes.
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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, 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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Done! 10651 genes of 11667 successfully translated.
Couldn't find Entrez IDs for 1016 genes.
Done! 16975 genes of 17527 successfully translated.
Couldn't find Entrez IDs for 552 genes.
Done! 10651 genes of 11667 successfully translated.
Couldn't find Entrez IDs for 1016 genes.
RUNIT TEST PROTOCOL -- Tue Apr 09 06:26:50 2019
***********************************************
Number of test functions: 11
Number of errors: 1
Number of failures: 0
1 Test Suite :
TFEA.ChIP RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_contingency_matrix: Error in get_chip_index(TFfilter = "EPAS1") :
No ChIP-Seq dataset in the database follows your conditions.
Test files with failing tests
test_TFEA.ChIP.R
test_contingency_matrix
Error in BiocGenerics:::testPackage(pkgname = "TFEA.ChIP") :
unit tests failed for package TFEA.ChIP
Execution halted
|
TFEA.ChIP.Rcheck/tests_x64/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(pkgname = "TFEA.ChIP")
Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from the ENCODE project.
To download the full ReMap database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Done! 2 genes of 2 successfully translated.
Done! 1 genes of 1 successfully translated.
Done! 1 genes of 1 successfully translated.
Done! 2 genes of 2 successfully translated.
Timing stopped at: 9.43 0.2 9.64
Error in get_chip_index(TFfilter = "EPAS1") :
No ChIP-Seq dataset in the database follows your conditions.
In addition: Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
Done! 16975 genes of 17527 successfully translated.
Couldn't find Entrez IDs for 552 genes.
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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, 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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Done! 10651 genes of 11667 successfully translated.
Couldn't find Entrez IDs for 1016 genes.
Done! 16975 genes of 17527 successfully translated.
Couldn't find Entrez IDs for 552 genes.
Done! 10651 genes of 11667 successfully translated.
Couldn't find Entrez IDs for 1016 genes.
RUNIT TEST PROTOCOL -- Tue Apr 09 06:27:42 2019
***********************************************
Number of test functions: 11
Number of errors: 1
Number of failures: 0
1 Test Suite :
TFEA.ChIP RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_contingency_matrix: Error in get_chip_index(TFfilter = "EPAS1") :
No ChIP-Seq dataset in the database follows your conditions.
Test files with failing tests
test_TFEA.ChIP.R
test_contingency_matrix
Error in BiocGenerics:::testPackage(pkgname = "TFEA.ChIP") :
unit tests failed for package TFEA.ChIP
Execution halted
|
|
TFEA.ChIP.Rcheck/examples_i386/TFEA.ChIP-Ex.timings
|
TFEA.ChIP.Rcheck/examples_x64/TFEA.ChIP-Ex.timings
|