Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).

CHECK results for S4Vectors on nebbiolo1

To the developers/maintainers of the S4Vectors package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/S4Vectors.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1660/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
S4Vectors 0.30.2  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/S4Vectors
git_branch: RELEASE_3_13
git_last_commit: 87b7827
git_last_commit_date: 2021-09-30 15:17:43 -0400 (Thu, 30 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: S4Vectors
Version: 0.30.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings S4Vectors_0.30.2.tar.gz
StartedAt: 2021-10-14 11:27:08 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:28:31 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 83.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: S4Vectors.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings S4Vectors_0.30.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/S4Vectors.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.30.2’
* 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:
  ‘I’ ‘head.LLint’ ‘pcompareRecursively’ ‘sort.List’ ‘t.HitsList’
  ‘tail.LLint’ ‘unname’ ‘window.LLint’
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 '[' and siglist 'LLint'
  generic '[<-' and siglist 'Rle'
  generic 'anyNA' and siglist 'List'
  generic 'by' and siglist 'Vector'
  generic 'coerce' and siglist 'ANY,DataFrame_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 'extractCOLS' and siglist 'DataFrame'
  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 '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 '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 'list,List'
  generic 'max' and siglist 'NSBS'
  generic 'mergeROWS' and siglist 'ANY'
  generic 'mergeROWS' and siglist 'DataFrame'
  generic 'mergeROWS' and siglist 'Vector'
  generic 'normalizeSingleBracketReplacementValue' and siglist
    'DataFrame'
  generic 'normalizeSingleBracketReplacementValue' and siglist 'List'
  generic 'order' and siglist 'List'
  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 'rep.int' and siglist 'LLint'
  generic 'rep' and siglist 'DataFrame'
  generic 'replaceCOLS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'ANY'
  generic 'replaceROWS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'replaceROWS' and siglist 'Vector'
  generic 'sameAsPreviousROW' and siglist 'Rle'
  generic 'sameAsPreviousROW' and siglist 'atomic'
  generic 'sameAsPreviousROW' and siglist 'complex'
  generic 'sameAsPreviousROW' and siglist 'integer'
  generic 'sameAsPreviousROW' and siglist 'numeric'
  generic 'sort' and siglist 'List'
  generic 'splitAsList' and siglist 'ANY'
  generic 'splitAsList' and siglist 'SortedByQueryHits'
  generic 'summary' and siglist 'FilterResults'
  generic 't' and siglist 'Pairs'
  generic 'tail' and siglist 'LLint'
  generic 'to' and siglist 'HitsList'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'window' and siglist 'LLint'
  generic 'with' and siglist 'Vector'
  generic 'xtabs' and siglist 'Vector'
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
shiftApply-methods 14.236  0.435  14.676
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/S4Vectors.Rcheck/00check.log’
for details.



Installation output

S4Vectors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL S4Vectors
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function ‘Hits_new’:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1549:20: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1549 | #define defineVar  Rf_defineVar
      |                    ^~~~~~~~~~~~
Hits_class.c:216:12: note: ‘revmap’ was declared here
  216 |  SEXP ans, revmap, symbol;
      |            ^~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c LLint_class.c -o LLint_class.o
LLint_class.c: In function ‘llints_summary’:
LLint_class.c:775:35: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  775 |     if (res == NA_LLINT || in_elt > res)
      |                            ~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c List_class.c -o List_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function ‘Rle_real_runq’:
Rle_utils.c:701:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  701 |     if (count_na != 0)
      |     ^~
Rle_utils.c:703:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  703 |      q_index = roundingScale(window_len_na,
      |      ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c character_utils.c -o character_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c eval_utils.c -o eval_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c integer_utils.c -o integer_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c logical_utils.c -o logical_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c raw_utils.c -o raw_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function]
  263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc)
      |             ^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/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 raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ 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’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
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’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (S4Vectors)

Tests output

S4Vectors.Rcheck/tests/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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


RUNIT TEST PROTOCOL -- Thu Oct 14 11:28:26 2021 
*********************************************** 
Number of test functions: 68 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
S4Vectors RUnit Tests - 68 test functions, 0 errors, 0 failures
Number of test functions: 68 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In combineUniqueCols(X, Y, Z, use.names = FALSE) :
  different values in multiple instances of column 'dup', ignoring this
  column in DFrame 2
2: In combineUniqueCols(X, Y, Z) :
  different values for shared rows in multiple instances of column 'dup',
  ignoring this column in DFrame 2
> 
> proc.time()
   user  system elapsed 
  9.466   0.250   9.706 

Example timings

S4Vectors.Rcheck/S4Vectors-Ex.timings

nameusersystemelapsed
Annotated-class0.7350.0160.751
DataFrame-class0.2170.0200.237
DataFrame-combine0.2820.0110.294
DataFrame-comparison0.0600.0030.063
DataFrame-utils0.1070.0000.108
Factor-class0.1760.0120.188
FilterRules-class0.1030.0000.103
Hits-class0.0590.0080.067
Hits-comparison0.0330.0000.033
Hits-setops0.1100.0040.114
HitsList-class0.0780.0000.077
LLint-class0.0230.0040.027
List-class0.4390.0000.440
List-utils0.0710.0000.071
Pairs-class0.0410.0000.041
RectangularData-class0.0000.0000.001
Rle-class0.0530.0100.064
Rle-runstat0.1290.0050.133
Rle-utils0.0160.0000.016
SimpleList-class0.0290.0000.030
TransposedDataFrame-class3.6960.1203.816
Vector-class0.0020.0000.002
Vector-comparison0.0500.0120.062
Vector-merge1.1150.0561.171
Vector-setops000
aggregate-methods0.1050.0040.109
character-utils0.0000.0030.004
expand-methods0.4270.0320.459
integer-utils0.0010.0000.002
isSorted0.0010.0030.004
shiftApply-methods14.236 0.43514.676
splitAsList0.0630.0000.064
stack-methods0.0490.0000.048
zip-methods0.0150.0000.015