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CHECK report for GOTHiC on tokay2

This page was generated on 2019-04-09 12:14:39 -0400 (Tue, 09 Apr 2019).

Package 693/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOTHiC 1.19.2
Borbala Mifsud
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GOTHiC
Branch: master
Last Commit: 911fb6f
Last Changed Date: 2019-01-04 13:35:01 -0400 (Fri, 04 Jan 2019)
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 

Summary

Package: GOTHiC
Version: 1.19.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOTHiC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GOTHiC_1.19.2.tar.gz
StartedAt: 2019-04-09 03:17:52 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:23:05 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 313.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GOTHiC.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOTHiC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GOTHiC_1.19.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOTHiC.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 'GOTHiC/DESCRIPTION' ... OK
* this is package 'GOTHiC' version '1.19.2'
* 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 'GOTHiC' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GOTHiC' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOTHiC.Rcheck/00install.out' for details.
* 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 ... WARNING
'::' or ':::' import not declared from: 'BiocManager'
'loadNamespace' or 'requireNamespace' call not declared from: 'BiocManager'
':::' call which should be '::': 'S4Vectors:::orderIntegerPairs'
  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
.binInteractions: no visible binding for global variable 'chr1'
.binInteractions: no visible binding for global variable 'chr2'
.binInteractions: no visible binding for global variable 'locus1'
.binInteractions: no visible binding for global variable 'locus2'
.binomialHiC: no visible binding for global variable 'resGR'
.binomialHiC : <anonymous>: no visible binding for global variable
  'frequencies'
.binomialHiC : <anonymous>: no visible binding for global variable
  'int1'
.binomialHiC : <anonymous>: no visible binding for global variable
  'int2'
.binomialHiC: no visible binding for global variable 'V1'
.binomialHiC: no visible binding for global variable 'int1'
.binomialHiC: no visible binding for global variable 'int2'
.binomialHiC: no visible binding for global variable 'frequencies'
.binomialHiC : <anonymous>: no visible global function definition for
  'binom.test'
.binomialHiC: no visible global function definition for 'p.adjust'
.binomialHiC: no visible binding for global variable 'pvalue'
.binomialHiC: no visible global function definition for 'x11'
.binomialHiC : <anonymous>: no visible global function definition for
  'pdf'
.binomialHiC : <anonymous>: no visible global function definition for
  'dev.off'
.binomialHiChicup : <anonymous>: no visible binding for global variable
  'frequencies'
.binomialHiChicup : <anonymous>: no visible binding for global variable
  'int1'
.binomialHiChicup : <anonymous>: no visible binding for global variable
  'int2'
.binomialHiChicup: no visible binding for global variable 'V1'
.binomialHiChicup: no visible binding for global variable 'int1'
.binomialHiChicup: no visible binding for global variable 'int2'
.binomialHiChicup: no visible binding for global variable 'frequencies'
.binomialHiChicup : <anonymous>: no visible global function definition
  for 'binom.test'
.binomialHiChicup: no visible global function definition for 'p.adjust'
.binomialHiChicup: no visible binding for global variable 'pvalue'
.binomialHiChicup: no visible global function definition for 'x11'
.binomialHiChicup : <anonymous>: no visible global function definition
  for 'pdf'
.binomialHiChicup : <anonymous>: no visible global function definition
  for 'dev.off'
.findOverlaps.circle: no visible global function definition for
  'IntervalTree'
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for 'isCircular'
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for 'seqlengths'
.getHindIIIsitesFromHicup: no visible global function definition for
  'read.table'
.getRestrictionSitesFromBSgenome: no visible global function definition
  for 'install.packages'
.getRestrictionSitesFromBSgenome: no visible global function definition
  for 'seqlengths'
.importHicup: no visible global function definition for 'read.table'
.onlyPairing: no visible global function definition for 'read.table'
.onlyPairing: no visible global function definition for 'ScanBamParam'
GOTHiC: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
GOTHiC: no visible binding for global variable 'filtered'
GOTHiC: no visible binding for global variable 'interactingLoci'
mapReadsToRestrictionSites: no visible binding for global variable
  'resGR'
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19 IntervalTree ScanBamParam V1 binom.test
  chr1 chr2 dev.off filtered frequencies install.packages int1 int2
  interactingLoci isCircular locus1 locus2 p.adjust pdf pvalue
  read.table resGR seqlengths x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "x11")
  importFrom("stats", "binom.test", "p.adjust")
  importFrom("utils", "install.packages", "read.table")
to your NAMESPACE file.
* 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 'GOTHiC-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GOTHiC
> ### Title: Genome Organisation Through HiC
> ### Aliases: GOTHiC
> ### Keywords: manip package
> 
> ### ** Examples
> 
> library(GOTHiC)
> dirPath <- system.file("extdata", package="HiCDataLymphoblast")
> fileName1 <- list.files(dirPath, full.names=TRUE)[1]
> fileName2 <- list.files(dirPath, full.names=TRUE)[2]
> binom=GOTHiC(fileName1, fileName2, sampleName='lymphoid_chr20', res=1000000, 
+ BSgenomeName='BSgenome.Hsapiens.UCSC.hg18', genome=BSgenome.Hsapiens.UCSC.hg18, 
+ restrictionSite='A^AGCTT', enzyme='HindIII',cistrans='all', filterdist=10000, 
+ DUPLICATETHRESHOLD=1, fileType='Table', parallel=FALSE, cores=NULL)
Pairing reads
Mapping reads to restriction sites
Error: RangedData objects are deprecated and the coercion method from RleList
  to RangedData is now defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GOTHiC-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GOTHiC
> ### Title: Genome Organisation Through HiC
> ### Aliases: GOTHiC
> ### Keywords: manip package
> 
> ### ** Examples
> 
> library(GOTHiC)
> dirPath <- system.file("extdata", package="HiCDataLymphoblast")
> fileName1 <- list.files(dirPath, full.names=TRUE)[1]
> fileName2 <- list.files(dirPath, full.names=TRUE)[2]
> binom=GOTHiC(fileName1, fileName2, sampleName='lymphoid_chr20', res=1000000, 
+ BSgenomeName='BSgenome.Hsapiens.UCSC.hg18', genome=BSgenome.Hsapiens.UCSC.hg18, 
+ restrictionSite='A^AGCTT', enzyme='HindIII',cistrans='all', filterdist=10000, 
+ DUPLICATETHRESHOLD=1, fileType='Table', parallel=FALSE, cores=NULL)
Pairing reads
Mapping reads to restriction sites
Error: RangedData objects are deprecated and the coercion method from RleList
  to RangedData is now defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
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 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOTHiC.Rcheck/00check.log'
for details.

Installation output

GOTHiC.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/GOTHiC_1.19.2.tar.gz && rm -rf GOTHiC.buildbin-libdir && mkdir GOTHiC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOTHiC.buildbin-libdir GOTHiC_1.19.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GOTHiC_1.19.2.zip && rm GOTHiC_1.19.2.tar.gz GOTHiC_1.19.2.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2160k  100 2160k    0     0  4267k      0 --:--:-- --:--:-- --:--:-- 4321k

install for i386

* installing *source* package 'GOTHiC' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GOTHiC'
    finding HTML links ... done
    GOTHiC                                  html  
    GOTHiChicup                             html  
    filtered                                html  
    mapReadsToRestrictionSites              html  
    pairReads                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GOTHiC' is deprecated and will be removed from Bioconductor
  version 3.10
** testing if installed package can be loaded from final location
Warning: Package 'GOTHiC' is deprecated and will be removed from Bioconductor
  version 3.10
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GOTHiC' ...
** testing if installed package can be loaded
Warning: Package 'GOTHiC' is deprecated and will be removed from Bioconductor
  version 3.10
* MD5 sums
packaged installation of 'GOTHiC' as GOTHiC_1.19.2.zip
* DONE (GOTHiC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GOTHiC' successfully unpacked and MD5 sums checked

Tests output

Example timings

GOTHiC.Rcheck/examples_i386/GOTHiC-Ex.timings

nameusersystemelapsed

GOTHiC.Rcheck/examples_x64/GOTHiC-Ex.timings

nameusersystemelapsed