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CHECK report for EventPointer on tokay2

This page was generated on 2019-10-16 12:37:55 -0400 (Wed, 16 Oct 2019).

Package 523/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EventPointer 2.2.4
Juan Pablo Romero
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/EventPointer
Branch: RELEASE_3_9
Last Commit: ff24eb8
Last Changed Date: 2019-06-03 12:33:12 -0400 (Mon, 03 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EventPointer
Version: 2.2.4
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_2.2.4.tar.gz
StartedAt: 2019-10-16 03:36:55 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:46:47 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 591.9 seconds
RetCode: 0
Status:  OK  
CheckDir: EventPointer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_2.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EventPointer.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.2.4'
* 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              5.76   0.03    6.07
CDFfromGTF_Multipath    5.16   0.52    5.68
EventDetection          0.15   0.00   14.39
EventDetectionMultipath 0.10   0.00   16.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
CDFfromGTF              7.47   0.03    7.50
EventDetectionMultipath 0.16   0.04   19.36
EventDetection          0.07   0.03   18.82
* 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-3.9-bioc/meat/EventPointer.Rcheck/00check.log'
for details.



Installation output

EventPointer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/EventPointer_2.2.4.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_2.2.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL EventPointer_2.2.4.zip && rm EventPointer_2.2.4.tar.gz EventPointer_2.2.4.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
 93  766k   93  720k    0     0  10.6M      0 --:--:-- --:--:-- --:--:-- 11.7M
100  766k  100  766k    0     0  11.1M      0 --:--:-- --:--:-- --:--:-- 12.2M

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
** 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_2.2.4.zip
* DONE (EventPointer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'EventPointer' successfully unpacked and MD5 sums checked

Tests output

EventPointer.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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, 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******


RUNIT TEST PROTOCOL -- Wed Oct 16 03:45:48 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  17.95    1.46   53.14 

EventPointer.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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, 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******


RUNIT TEST PROTOCOL -- Wed Oct 16 03:46:41 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  19.65    0.76   52.32 

Example timings

EventPointer.Rcheck/examples_i386/EventPointer-Ex.timings

nameusersystemelapsed
CDFfromGTF5.760.036.07
CDFfromGTF_Multipath5.160.525.68
EventDetection 0.15 0.0014.39
EventDetectionMultipath 0.10 0.0016.44
EventPointer0.040.010.08
EventPointer_IGV2.140.022.16
EventPointer_RNASeq0.080.000.08
EventPointer_RNASeq_IGV3.030.093.14
EventPointer_RNASeq_TranRef0.010.000.02
EventsGTFfromTrancriptomeGTF3.320.013.36
FindPrimers000
GetPSI_FromTranRef0.010.000.06
PSI_Statistic0.140.040.25
PrepareBam_EP000
getbootstrapkallisto0.320.140.64

EventPointer.Rcheck/examples_x64/EventPointer-Ex.timings

nameusersystemelapsed
CDFfromGTF7.470.037.50
CDFfromGTF_Multipath4.410.004.41
EventDetection 0.07 0.0318.82
EventDetectionMultipath 0.16 0.0419.36
EventPointer0.090.010.11
EventPointer_IGV2.860.022.87
EventPointer_RNASeq0.080.000.08
EventPointer_RNASeq_IGV3.000.013.01
EventPointer_RNASeq_TranRef0.000.020.02
EventsGTFfromTrancriptomeGTF3.80.03.8
FindPrimers000
GetPSI_FromTranRef0.050.000.04
PSI_Statistic0.140.010.16
PrepareBam_EP0.000.000.02
getbootstrapkallisto0.310.100.40