Bioconductor Package Maintainer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/S4Vectors |
| Branch: RELEASE_3_9 |
| Last Commit: d25e517 |
| Last Changed Date: 2019-09-04 04:27:04 -0400 (Wed, 04 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:04:33 -0400 (Wed, 16 Oct 2019).
| Package 1445/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| S4Vectors 0.22.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: S4Vectors |
| Version: 0.22.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings S4Vectors_0.22.1.tar.gz |
| StartedAt: 2019-10-16 04:45:34 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:47:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 95.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: S4Vectors.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings S4Vectors_0.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/S4Vectors.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘0.22.1’ * 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 :: 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’ ‘transform.Vector’ ‘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 '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 'Rle,NSBS' generic 'extractROWS' and siglist 'Rle,RleNSBS' 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 '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 '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' 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 '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 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 11.103 0.328 11.47 * 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-3.9-bioc/meat/S4Vectors.Rcheck/00check.log’ for details.
S4Vectors.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL S4Vectors
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/include/Rdefines.h:40:0,
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-3.9-bioc/R/include/Rinternals.h:1402:20: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define defineVar Rf_defineVar
^~~~~~~~~~~~
Hits_class.c:216:12: note: ‘revmap’ was declared here
SEXP ans, revmap, symbol;
^~~~~~
Hits_class.c: In function ‘select_hits’:
Hits_class.c:346:24: warning: ‘is_used’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (nodup0 && is_used->elts[ans_elt - 1])
~~~~~~~^~~~~~
gcc -I"/home/biocbuild/bbs-3.9-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]
if (res == NA_LLINT || in_elt > res)
~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-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]
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’
q_index = roundingScale(window_len_na,
^~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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]
static void sort_uchar_array(unsigned char *x, int nelt, int desc)
^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 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 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)
S4Vectors.Rcheck/tests/run_unitTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
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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, 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 -- Wed Oct 16 04:46:58 2019
***********************************************
Number of test functions: 62
Number of errors: 0
Number of failures: 0
1 Test Suite :
S4Vectors RUnit Tests - 62 test functions, 0 errors, 0 failures
Number of test functions: 62
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.971 0.172 12.348
S4Vectors.Rcheck/S4Vectors-Ex.timings
| name | user | system | elapsed | |
| Annotated-class | 0.863 | 0.027 | 0.893 | |
| DataFrame-class | 0.366 | 0.009 | 0.378 | |
| DataTable-class | 0.036 | 0.000 | 0.037 | |
| FilterRules-class | 0.156 | 0.000 | 0.156 | |
| Hits-class | 0.060 | 0.003 | 0.065 | |
| Hits-comparison | 0.025 | 0.005 | 0.029 | |
| Hits-setops | 0.095 | 0.000 | 0.095 | |
| LLint-class | 0.028 | 0.000 | 0.029 | |
| List-class | 0.001 | 0.000 | 0.001 | |
| List-utils | 0.093 | 0.003 | 0.098 | |
| Pairs-class | 0.048 | 0.001 | 0.048 | |
| Rle-class | 0.063 | 0.000 | 0.063 | |
| Rle-runstat | 0.145 | 0.000 | 0.146 | |
| Rle-utils | 0.014 | 0.000 | 0.015 | |
| SimpleList-class | 0.022 | 0.000 | 0.022 | |
| Vector-class | 0.001 | 0.000 | 0.001 | |
| Vector-comparison | 0.036 | 0.000 | 0.037 | |
| Vector-merge | 1.257 | 0.055 | 1.313 | |
| Vector-setops | 0 | 0 | 0 | |
| aggregate-methods | 0.096 | 0.000 | 0.096 | |
| character-utils | 0.003 | 0.000 | 0.003 | |
| expand-methods | 0.337 | 0.000 | 0.337 | |
| integer-utils | 0.001 | 0.000 | 0.001 | |
| isSorted | 0.004 | 0.000 | 0.004 | |
| shiftApply-methods | 11.103 | 0.328 | 11.470 | |
| split-methods | 0.067 | 0.000 | 0.067 | |
| zip-methods | 0.014 | 0.000 | 0.014 | |