Juan Pablo Romero
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/EventPointer |
| Branch: RELEASE_3_12 |
| Last Commit: bde3577 |
| Last Changed Date: 2020-10-27 11:21:53 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:04 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the EventPointer package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 573/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EventPointer 2.8.0 (landing page) Juan Pablo Romero
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: EventPointer |
| Version: 2.8.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EventPointer.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings EventPointer_2.8.0.tar.gz |
| StartedAt: 2021-05-06 02:40:39 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:53:25 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 766.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EventPointer.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EventPointer.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings EventPointer_2.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/EventPointer.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.8.0'
* 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 (user + system) or elapsed time > 5s
user system elapsed
CDFfromGTF 6.27 0.40 6.67
EventsGTFfromTrancriptomeGTF 5.52 0.03 5.82
CDFfromGTF_Multipath 5.00 0.02 5.01
EventDetectionMultipath 0.08 0.02 16.67
EventDetection 0.05 0.01 20.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CDFfromGTF 11.72 0.06 12.39
CDFfromGTF_Multipath 8.16 0.00 8.20
EventsGTFfromTrancriptomeGTF 5.11 0.00 5.11
EventDetection 0.16 0.02 21.34
EventDetectionMultipath 0.15 0.00 21.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/EventPointer.Rcheck/00check.log'
for details.
EventPointer.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/EventPointer_2.8.0.tar.gz && rm -rf EventPointer.buildbin-libdir && mkdir EventPointer.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EventPointer.buildbin-libdir EventPointer_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL EventPointer_2.8.0.zip && rm EventPointer_2.8.0.tar.gz EventPointer_2.8.0.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 24.6M 0 --:--:-- --:--:-- --:--:-- 25.7M
install for i386
* installing *source* package 'EventPointer' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** 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
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** 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
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
* MD5 sums
packaged installation of 'EventPointer' as EventPointer_2.8.0.zip
* DONE (EventPointer)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'EventPointer' successfully unpacked and MD5 sums checked
|
EventPointer.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, 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
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
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******
RUNIT TEST PROTOCOL -- Thu May 06 02:51:57 2021
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
EventPointer RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
>
> proc.time()
user system elapsed
21.87 1.57 64.96
|
EventPointer.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, 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
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
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******
RUNIT TEST PROTOCOL -- Thu May 06 02:53:17 2021
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
EventPointer RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
>
> proc.time()
user system elapsed
28.54 0.93 79.43
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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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