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CHECK report for S4Vectors on merida2

This page was generated on 2018-10-17 08:52:59 -0400 (Wed, 17 Oct 2018).

Package 1305/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
S4Vectors 0.18.3
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/S4Vectors
Branch: RELEASE_3_7
Last Commit: d6804f9
Last Changed Date: 2018-06-07 11:08:23 -0400 (Thu, 07 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: S4Vectors
Version: 0.18.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings S4Vectors_0.18.3.tar.gz
StartedAt: 2018-10-16 23:53:37 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:55:07 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 90.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: S4Vectors.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings S4Vectors_0.18.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/S4Vectors.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.18.3’
* package encoding: UTF-8
* 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 ‘S4Vectors’ 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
* 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:
  ‘data.table:::as.data.frame.data.table’
  ‘stats:::na.exclude.data.frame’ ‘stats:::na.omit.data.frame’
  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
evalSeparately,FilterRules : <anonymous>: no visible global function
  definition for ‘.’
Undefined global functions or variables:
  .
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Vector-comparison.Rd':
  ‘[IRanges]{IntegerRanges-comparison}’

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘cbind.DataFrame’ ‘head.LLint’ ‘pcompareRecursively’ ‘phead’ ‘ptail’
  ‘rbind.DataFrame’ ‘selectHits’ ‘t.Hits’ ‘t.HitsList’ ‘tail.LLint’
  ‘window.LLint’
Undocumented S4 classes:
  ‘integer_OR_LLint’ ‘list_OR_List’
Undocumented S4 methods:
  generic '!' and siglist 'List'
  generic '<=' and siglist 'List,List'
  generic '<=' and siglist 'List,list'
  generic '<=' and siglist 'list,List'
  generic '==' and siglist 'List,List'
  generic '==' and siglist 'List,list'
  generic '==' and siglist 'list,List'
  generic 'NSBS' and siglist 'Rle'
  generic '[' and siglist 'LLint'
  generic 'anyDuplicated' and siglist 'Rle'
  generic 'anyDuplicated' and siglist 'RleNSBS'
  generic 'anyNA' and siglist 'List'
  generic 'anyNA' and siglist 'Rle'
  generic 'as.integer' and siglist 'RleNSBS'
  generic 'by' and siglist 'Vector'
  generic 'coerce' and siglist 'ANY,DataTable_OR_NULL'
  generic 'countMatches' and siglist 'ANY'
  generic 'do.call' and siglist 'ANY,List'
  generic 'droplevels' and siglist 'DataFrame'
  generic 'duplicated' and siglist 'List'
  generic 'eval' and siglist 'expression,Vector'
  generic 'eval' and siglist 'language,Vector'
  generic 'extractROWS' and siglist 'DataFrame,ANY'
  generic 'extractROWS' and siglist 'LLint,ANY'
  generic 'extractROWS' and siglist 'LLint,NSBS'
  generic 'extractROWS' and siglist 'LLint,RangeNSBS'
  generic 'extractROWS' and siglist 'Rle,NSBS'
  generic 'extractROWS' and siglist 'Rle,RleNSBS'
  generic 'extractROWS' and siglist 'SortedByQueryHits,ANY'
  generic 'extractROWS' and siglist 'Vector,ANY'
  generic 'filterRules' and siglist 'FilterResults'
  generic 'from' and siglist 'HitsList'
  generic 'getListElement' and siglist 'SimpleList'
  generic 'grep' and siglist 'ANY,Rle'
  generic 'grepl' and siglist 'ANY,Rle'
  generic 'head' and siglist 'LLint'
  generic 'is.na' and siglist 'List'
  generic 'is.unsorted' and siglist 'List'
  generic 'isStrictlySorted' and siglist 'Rle'
  generic 'isStrictlySorted' and siglist 'RleNSBS'
  generic 'length' and siglist 'RleNSBS'
  generic 'match' and siglist 'ANY,Rle'
  generic 'match' and siglist 'List,List'
  generic 'match' and siglist 'List,Vector'
  generic 'match' and siglist 'List,list'
  generic 'match' and siglist 'List,vector'
  generic 'match' and siglist 'Rle,Rle'
  generic 'match' and siglist 'list,List'
  generic 'order' and siglist 'List'
  generic 'order' and siglist 'Rle'
  generic 'pcompare' and siglist 'List,List'
  generic 'pcompare' and siglist 'List,list'
  generic 'pcompare' and siglist 'list,List'
  generic 'pcompareRecursively' and siglist 'List'
  generic 'pcompareRecursively' and siglist 'list'
  generic 'rank' and siglist 'List'
  generic 'rank' and siglist 'Rle'
  generic 'rep.int' and siglist 'LLint'
  generic 'rep.int' and siglist 'Vector'
  generic 'rep' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'sort' and siglist 'DataTable'
  generic 'sort' and siglist 'List'
  generic 'sort' and siglist 'SortedByQueryHits'
  generic 'summary' and siglist 'FilterResults'
  generic 't' and siglist 'Pairs'
  generic 'tail' and siglist 'LLint'
  generic 'to' and siglist 'HitsList'
  generic 'transform' and siglist 'Vector'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'updateObject' and siglist 'Vector'
  generic 'window' and siglist 'LLint'
  generic 'with' and siglist 'Vector'
  generic 'xtabs' and siglist 'Vector'
  generic 'xtfrm' and siglist 'Rle'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
shiftApply-methods 10.226  1.114  11.701
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/S4Vectors.Rcheck/00check.log’
for details.



Installation output

S4Vectors.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL S4Vectors
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘S4Vectors’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c AEbufs.c -o AEbufs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DataFrame_class.c -o DataFrame_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Hits_class.c -o Hits_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c LLint_class.c -o LLint_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c List_class.c -o List_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rle_class.c -o Rle_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rle_utils.c -o Rle_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c SEXP_utils.c -o SEXP_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c SimpleList_class.c -o SimpleList_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c anyMissing.c -o anyMissing.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c character_utils.c -o character_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c eval_utils.c -o eval_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hash_utils.c -o hash_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c integer_utils.c -o integer_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c logical_utils.c -o logical_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c safe_arithm.c -o safe_arithm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: unused function 'sort_uchar_array' [-Wunused-function]
static void sort_uchar_array(unsigned char *x, int nelt, int desc)
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c subsetting_utils.c -o subsetting_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vector_utils.c -o vector_utils.o
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 S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DataFrame"’: no definition for class “data.table”
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RleTricks.Rnw’ using ‘UTF-8’ 
   ‘S4QuickOverview.Rnw’ using ‘UTF-8’ 
   ‘S4VectorsOverview.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (S4Vectors)

Tests output

S4Vectors.Rcheck/tests/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> require("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
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


Attaching package: 'S4Vectors'

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

    expand.grid

[1] TRUE
> S4Vectors:::.test()
Loading required package: GenomeInfoDb


RUNIT TEST PROTOCOL -- Tue Oct 16 23:55:00 2018 
*********************************************** 
Number of test functions: 60 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
S4Vectors RUnit Tests - 60 test functions, 0 errors, 0 failures
Number of test functions: 60 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  9.611   0.295   9.961 

Example timings

S4Vectors.Rcheck/S4Vectors-Ex.timings

nameusersystemelapsed
Annotated-class0.7510.0450.797
DataFrame-class0.2770.0090.287
DataTable-class0.0280.0010.030
FilterRules-class0.1370.0010.139
Hits-class0.1060.0020.109
Hits-comparison0.0310.0000.032
Hits-setops0.1170.0020.120
LLint-class0.0590.0050.064
List-class0.0030.0000.003
List-utils0.1330.0020.135
Pairs-class0.0520.0000.052
Rle-class0.0840.0010.085
Rle-runstat0.1690.0020.172
Rle-utils0.0270.0010.028
SimpleList-class0.0280.0010.031
Vector-class0.0040.0010.004
Vector-comparison0.0630.0010.065
Vector-merge1.6860.0831.783
Vector-setops0.0010.0000.001
aggregate-methods0.1120.0020.117
character-utils0.0050.0010.007
expand-methods0.2310.0030.235
integer-utils0.0040.0000.004
isSorted0.0080.0000.008
shiftApply-methods10.226 1.11411.701
split-methods0.0670.0020.069
zip-methods0.0170.0010.018