| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:29:52 -0400 (Tue, 09 Apr 2019).
| Package 514/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EventPointer 2.1.4 Juan Pablo Romero
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| 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: EventPointer |
| Version: 2.1.4 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EventPointer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EventPointer_2.1.4.tar.gz |
| StartedAt: 2019-04-09 02:37:18 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:47:00 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 582.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: EventPointer.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EventPointer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EventPointer_2.1.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EventPointer.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 'EventPointer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EventPointer' version '2.1.4'
* 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 'EventPointer' 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 ... NOTE
Unexported objects imported by ':::' calls:
'SGSeq:::addFeatureID' 'SGSeq:::addGeneID' 'SGSeq:::edges'
'SGSeq:::exonGraph' 'SGSeq:::feature2name' 'SGSeq:::matchSGFeatures'
'SGSeq:::nodes' 'SGSeq:::propagateAnnotation'
'SGSeq:::splitCharacterList'
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
annotate2: no visible global function definition for
'addDummySpliceSites'
annotate2: no visible global function definition for 'annotatePaths'
annotateFeatures2: no visible global function definition for
'matchTxFeatures'
Undefined global functions or variables:
addDummySpliceSites annotatePaths matchTxFeatures
* 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
CDFfromGTF 4.56 0.04 6.03
EventDetection 0.08 0.03 14.34
EventDetectionMultipath 0.10 0.00 16.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CDFfromGTF 6.49 0.03 6.52
EventDetectionMultipath 0.12 0.04 13.67
EventDetection 0.08 0.00 14.19
* 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 :
EventPointer RUnit Tests - 14 test functions, 0 errors, 1 failure
FAILURE in test_FindPrimers: Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", :
FALSE
Test files with failing tests
test_FindPrimers.R
test_FindPrimers
Error in BiocGenerics:::testPackage("EventPointer") :
unit tests failed for package EventPointer
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 :
EventPointer RUnit Tests - 14 test functions, 0 errors, 1 failure
FAILURE in test_FindPrimers: Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", :
FALSE
Test files with failing tests
test_FindPrimers.R
test_FindPrimers
Error in BiocGenerics:::testPackage("EventPointer") :
unit tests failed for package EventPointer
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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/EventPointer.Rcheck/00check.log'
for details.
EventPointer.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/EventPointer_2.1.4.tar.gz && rm -rf EventPointer.buildbin-libdir && mkdir EventPointer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EventPointer.buildbin-libdir EventPointer_2.1.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL EventPointer_2.1.4.zip && rm EventPointer_2.1.4.tar.gz EventPointer_2.1.4.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 764k 100 764k 0 0 10.4M 0 --:--:-- --:--:-- --:--:-- 11.4M
install for i386
* installing *source* package 'EventPointer' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'EventPointer'
finding HTML links ... done
AllEvents_RNASeq html
AllEvents_RNASeq_MP html
ArrayDatamultipath html
ArraysData html
CDFfromGTF html
CDFfromGTF_Multipath html
EventDetection html
EventDetectionMultipath html
EventPointer html
EventPointer_IGV html
EventPointer_RNASeq html
EventPointer_RNASeq_IGV html
EventPointer_RNASeq_TranRef html
EventXtrans html
EventsGTFfromTrancriptomeGTF html
FindPrimers html
GetPSI_FromTranRef html
InternalFunctions html
MyPrimers html
MyPrimers_taqman html
PSI_Statistic html
PSIss html
PrepareBam_EP html
SG_RNASeq html
getbootstrapkallisto 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 'EventPointer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EventPointer' as EventPointer_2.1.4.zip
* DONE (EventPointer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'EventPointer' successfully unpacked and MD5 sums checked
|
EventPointer.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("EventPointer")
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Creating SG Information...Creating SG Information...
Obtaining Events
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Obtaining Events
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Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
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Creating .txt ...
.txt created
Creating .GTF ...
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|======================= | 33%
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.txt created
Creating the sparseMatrix of paths x transcripts...
******FINISHED******
Timing stopped at: 0 0 0
Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", :
FALSE
RUNIT TEST PROTOCOL -- Tue Apr 09 02:45:56 2019
***********************************************
Number of test functions: 14
Number of errors: 0
Number of failures: 1
1 Test Suite :
EventPointer RUnit Tests - 14 test functions, 0 errors, 1 failure
FAILURE in test_FindPrimers: Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", :
FALSE
Test files with failing tests
test_FindPrimers.R
test_FindPrimers
Error in BiocGenerics:::testPackage("EventPointer") :
unit tests failed for package EventPointer
Execution halted
|
EventPointer.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("EventPointer")
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Creating SG Information...Creating SG Information...
Obtaining Events
|
| | 0%
Obtaining Events
|
| | 0%
Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Creating .txt ...
.txt created
Creating .GTF ...
|
| | 0%
|
|======== | 11%
|
|================ | 22%
|
|======================= | 33%
|
|=============================== | 44%
|
|======================================= | 56%
|
|=============================================== | 67%
|
|====================================================== | 78%
|
|============================================================== | 89%
|
|======================================================================| 100%
.txt created
Creating the sparseMatrix of paths x transcripts...
******FINISHED******
Timing stopped at: 0 0 0
Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", :
FALSE
RUNIT TEST PROTOCOL -- Tue Apr 09 02:46:49 2019
***********************************************
Number of test functions: 14
Number of errors: 0
Number of failures: 1
1 Test Suite :
EventPointer RUnit Tests - 14 test functions, 0 errors, 1 failure
FAILURE in test_FindPrimers: Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", :
FALSE
Test files with failing tests
test_FindPrimers.R
test_FindPrimers
Error in BiocGenerics:::testPackage("EventPointer") :
unit tests failed for package EventPointer
Execution halted
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EventPointer.Rcheck/examples_i386/EventPointer-Ex.timings
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EventPointer.Rcheck/examples_x64/EventPointer-Ex.timings
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