Package: annmap

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annmap_1.24.0.tar.gz

StartedAt: 2019-04-15 22:20:11 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:25:38 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 326.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: annmap.Rcheck

Warnings: 1

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annmap_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/annmap.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘annmap’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annmap’ 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' call to ‘rjson’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.make.hash’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.coerce: no visible global function definition for ‘setNames’
.coerce: no visible binding for global variable ‘v’
.coerce: no visible binding for global variable ‘k’
.get.stats.cache: no visible global function definition for
  ‘flush.console’
.layout.genes: no visible global function definition for ‘strwidth’
.load.and.parse: no visible global function definition for ‘fromJSON’
.read.databases: no visible global function definition for ‘read.table’
.single.transcript.coords.to.genome: no visible global function
  definition for ‘tail’
.xmc.connect: no visible global function definition for ‘menu’
.xmcws.connect: no visible global function definition for ‘fromJSON’
.xmcws.connect: no visible global function definition for ‘menu’
annmapAddConnection: no visible global function definition for
  ‘write.table’
annmapConnect: no visible global function definition for
  ‘install.packages’
arrayType: no visible global function definition for ‘menu’
convertBamToRle : <anonymous>: no visible global function definition
  for ‘Rle’
geneToGeneRegionTrack : generate: no visible global function definition
  for ‘GeneRegionTrack’
generateBridgeData: no visible global function definition for ‘rainbow’
genomicPlot : <anonymous>: no visible global function definition for
  ‘rgb’
genomicPlot: no visible global function definition for ‘rgb’
ngsTracePlotter : local.draw: no visible global function definition for
  ‘runValue’
ngsTracePlotter: no visible global function definition for ‘modifyList’
ngsTraceScale : <anonymous>: no visible global function definition for
  ‘runValue’
seqnameMapping: no visible global function definition for ‘seqlevels<-’
seqnameMapping: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  GeneRegionTrack Rle flush.console fromJSON install.packages k menu
  modifyList rainbow read.table rgb runValue seqlevels seqlevels<-
  setNames strwidth tail v write.table
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "strwidth")
  importFrom("stats", "setNames")
  importFrom("utils", "flush.console", "install.packages", "menu",
             "modifyList", "read.table", "tail", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plot.ngs.Rd':
  ‘[IRanges]{Rle}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/annmap.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annmap
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘annmap’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annmap)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> if( require( "RUnit", quietly=TRUE ) ) {
+   pkg <- "annmap"
+  
+   if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+     path <- file.path( getwd(), "..", "inst", "unitTests" )
+   }
+   else {
+     path <- system.file( package=pkg, "unitTests" )
+   }
+ 
+   cat( "\nRunning unit tests\n" )
+   print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+   library( package=pkg, character.only=TRUE )
+ 
+   annmapClearCache()
+ 
+   # Run the old style RangedData for tim...
+   #annmapSetParam( oldstylekey='P0fSpS' )
+   annmapSetParam( spacefn=if( annmap:::.usegranges() ) seqnames else space )
+   annmapSetParam( defaultclass=if( annmap:::.usegranges() ) 'GRanges' else 'RangedData' )
+ 
+   #Fail on warnings
+   options( warn=2 )
+ 
+   # Get the pattern (if there is one?)
+   patt = Sys.getenv( "RUNITFILEPATTERN" )
+   func = Sys.getenv( 'RUNITFUNCPATTERN' )
+   if( is.null( patt ) || nchar( patt ) == 0 ) {
+     patt = "^runit.+\\.[rR]$"
+   }
+   else {
+     patt = paste( "^runit\\.", patt, "\\.[rR]$", sep="" )
+   }
+   if( is.null( func ) || nchar( func ) == 0 ) {
+     func = "^test.+"
+   }
+   else {
+     func = paste( "^test\\.", func, ".+", sep="" )
+   }
+   testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=patt, testFuncRegexp=func, dirs=path )
+   tests <- runTestSuite( testSuite )
+  
+   pathReport <- file.path( path, "report" )
+  
+   cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+   printTextProtocol( tests, showDetails=FALSE )
+   printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+   printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+  
+   printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+  
+   tmp <- getErrors( tests )
+   if( tmp$nFail > 0 | tmp$nErr > 0 ) {
+     stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep="" ) )
+   }
+ } else {
+   warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "annmap"

$getwd
[1] "/Users/biocbuild/bbs-3.8-bioc/meat/annmap.Rcheck/tests"

$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/annmap/unitTests"

Loading required package: GenomicRanges
Loading required package: stats4
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, 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, lengths, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Using /Users/biocbuild/.annmap as our configuration directory.


Executing test function test.template  ...  done successfully.



Executing test function test.all.queries  ... [1] "\nSkipping allXXX tests, as not on a PICR machine"
 done successfully.



Executing test function test.gotsomefunctions  ...  done successfully.



Executing test function test.cache  ...  done successfully.



Executing test function test.ANNMAP112  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.huisun.ANNMAP48  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.chaining  ... [1] "Cannot find datasource 'hs-test' so skipping this test."
 done successfully.



Executing test function test.addConnection  ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
Connection a added. 
Connection b added. 
Connection a updated. 
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
 done successfully.



Executing test function test.buildsql  ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
 done successfully.



Executing test function test.connection  ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
[1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
 done successfully.



Executing test function test.databases.txt  ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
[1] "Mocking annmapConnect()"
[1] "setting conf.dir to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/annmap/unitTests/tabConfig"
[1] "setting conf.dir to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/annmap/unitTests/commaConfig"
[1] "restoring connect method"
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
 done successfully.



Executing test function test.details.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Cannot find datasource 'mm-test', so skipping these tests."
[1] "Cannot find datasource 'rn-test', so skipping these tests."
[1] "Cannot find datasource 'pb-test', so skipping these tests."
 done successfully.



Executing test function test.gotsomefunctions  ...  done successfully.



Executing test function test.filters  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.bug.ACBBUTIL33  ... [1] "Cannot find datasource 'mm-test', so skipping this test."
 done successfully.



Executing test function test.bug.ANNMAP40  ... [1] "Cannot find datasource 'hs-test', so skipping this test."
 done successfully.



Executing test function test.bug.ANNMAP44  ... [1] "Cannot find datasource 'hs-test', so skipping this test."
 done successfully.



Executing test function test.gotsomefunctions  ...  done successfully.



Executing test function test.multi.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.range.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Cannot find datasource 'mm-test', so skipping these tests."
[1] "Cannot find datasource 'rn-test', so skipping these tests."
[1] "Cannot find datasource 'pb-test', so skipping these tests."
 done successfully.



Executing test function test.expr.query  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.gotsomefunctions  ...  done successfully.



Executing test function test.to.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Cannot find datasource 'mm-test', so skipping these tests."
[1] "Cannot find datasource 'rn-test', so skipping these tests."
[1] "Cannot find datasource 'pb-test', so skipping these tests."
 done successfully.



Executing test function test.transcript.to.translatedprobes  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.ANNMAP.109  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.ANNMAP.97  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.ANNMAP.98  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.array.type  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.make.params  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.needs.array  ...  done successfully.



Executing test function test.rangeapply  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.reality  ...  done successfully.



Executing test function test.seqnames  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.set.get.params  ...  done successfully.



Executing test function test.ANNMAP118  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.michal.utr.bug  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.michal.utr.bug.three  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.michal.utr.bug.two  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.utr  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.yaoyong.utr.bug  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
 done successfully.



Executing test function test.ANNMAP33  ... [1] "\nSkipping webservice tests, no route to annmap website"
 done successfully.



Executing test function test.connection  ... [1] "\nSkipping webservice tests, no route to annmap website"
 done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Mon Apr 15 22:25:33 2019 
*********************************************** 
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
annmap unit testing - 42 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  7.677   0.495 160.293 

name	user	system	elapsed
annmap.all	0.000	0.000	0.001
annmap.coords	0.008	0.000	0.009
annmap.details	0.001	0.000	0.001
annmap.env	0.000	0.000	0.001
annmap.filters	0.002	0.000	0.003
annmap.range	0.001	0.001	0.002
annmap.seqname	0	0	0
annmap.spliceIndex	0.001	0.000	0.000
annmap.to	0.000	0.000	0.001
annmap.utils	0.001	0.000	0.001
annmap.utr	0	0	0