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BioC 3.4: CHECK report for biovizBase on morelia

This page was generated on 2016-09-21 03:51:17 -0700 (Wed, 21 Sep 2016).

Package 127/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.21.0
Michael Lawrence
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biovizBase
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  ERROR 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: biovizBase
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.21.0.tar.gz
StartedAt: 2016-09-20 03:46:32 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:50:21 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 228.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: biovizBase.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biovizBase_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biovizBase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* 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
'library' or 'require' calls in package code:
  'BSgenome' 'rtracklayer'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genSymbols: no visible binding for global variable 'start_location'
genSymbols: no visible binding for global variable 'end_location'
genSymbols: no visible binding for global variable 'Chromosome'
genSymbols: no visible binding for global variable 'symbol'
transformToLinkInCircle: no visible binding for global variable
  '.circle.x'
transformToLinkInCircle: no visible binding for global variable
  '.circle.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'from.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'from.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'to.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'to.y'
mold,ExpressionSet: no visible global function definition for 'exprs'
mold,ExpressionSet: no visible global function definition for 'pData'
mold,RleList: no visible binding for global variable 'xRleList'
mold,eSet: no visible global function definition for 'phenoData'
mold,eSet: no visible global function definition for 'melt'
mold,eSet: no visible global function definition for 'varLabels'
Undefined global functions or variables:
  .circle.x .circle.y Chromosome end_location exprs from.x from.y melt
  pData phenoData start_location symbol to.x to.y varLabels xRleList
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘biovizBase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crunch
> ### Title: Fetching GRanges from various data source
> ### Aliases: crunch crunch,TxDb-method crunch,EnsDb-method
> ###   crunch,GAlignments-method crunch,BamFile-method
> 
> ### ** Examples
> 
> library(biovizBase)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, 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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.

> data(genesymbol, package = "biovizBase")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> obj <- txdb
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "all")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "reduce")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
> 
> ## Fetching data from a EnsDb object.
> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
  call: validityMethod(object)
  error: could not find function "dbHasRequiredTables"
Error: package or namespace load failed for 'EnsDb.Hsapiens.v75'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  biovizBase RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/unitTests/test_ensdb.R: Error while sourcing  /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/unitTests/test_ensdb.R : Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
  
  Test files with failing tests
  
     test_ensdb.R 
       /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/unitTests/test_ensdb.R 
  
  
  Error in BiocGenerics:::testPackage("biovizBase") : 
    unit tests failed for package biovizBase
  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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

runTests.Rout.fail:


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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("biovizBase")
Loading required package: ensembldb
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, 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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.

Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
  call: validityMethod(object)
  error: could not find function "dbHasRequiredTables"
Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'


RUNIT TEST PROTOCOL -- Tue Sep 20 03:50:18 2016 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
biovizBase RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/unitTests/test_ensdb.R: Error while sourcing  /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/unitTests/test_ensdb.R : Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'

Test files with failing tests

   test_ensdb.R 
     /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/unitTests/test_ensdb.R 


Error in BiocGenerics:::testPackage("biovizBase") : 
  unit tests failed for package biovizBase
Execution halted

biovizBase.Rcheck/00install.out:

* installing *source* package ‘biovizBase’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_biovizBase.c -o R_init_biovizBase.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c:57:15: warning: passing 'Rbyte *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
  if (strncmp(b, "BAI\1", 4))
              ^
/usr/include/string.h:84:26: note: passing argument to parameter here
int      strncmp(const char *, const char *, size_t);
                             ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/biovizBase.Rcheck/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biovizBase)

biovizBase.Rcheck/biovizBase-Ex.timings:

nameusersystemelapsed
CRC0.0070.0010.007
GCcontent0.4970.0090.540
addStepping-method0.7140.0240.738
aes-utils0.0000.0000.001
colorBlindSafePal0.0010.0000.000
containLetters0.0000.0000.001
crc1.GeRL0.010.000.01