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
|