| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:21 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 1660/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| S4Vectors 0.30.2 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: S4Vectors |
| Version: 0.30.2 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:S4Vectors.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings S4Vectors_0.30.2.tar.gz |
| StartedAt: 2021-10-15 05:00:37 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:03:24 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 166.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: S4Vectors.Rcheck |
| Warnings: 3 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:S4Vectors.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings S4Vectors_0.30.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'S4Vectors' can be installed ... WARNING
Found the following significant warnings:
LLint_class.c:358:24: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/libs/i386/S4Vectors.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/libs/x64/S4Vectors.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shiftApply-methods 17.83 2 19.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shiftApply-methods 14.43 2.05 16.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
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: 3 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.Rcheck/00check.log'
for details.
S4Vectors.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/S4Vectors_0.30.2.tar.gz && rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=S4Vectors.buildbin-libdir S4Vectors_0.30.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.30.2.zip && rm S4Vectors_0.30.2.tar.gz S4Vectors_0.30.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 261k 100 261k 0 0 969k 0 --:--:-- --:--:-- --:--:-- 973k
install for i386
* installing *source* package 'S4Vectors' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_increase_buflength':
AEbufs.c:16:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '4294967296' to '0' [-Woverflow]
#define MAX_BUFLENGTH (128ULL * MAX_BUFLENGTH_INC) // 2^32
^
AEbufs.c:31:9: note: in expansion of macro 'MAX_BUFLENGTH'
return MAX_BUFLENGTH;
^~~~~~~~~~~~~
AEbufs.c: In function '_IntAEAE_toEnvir':
AEbufs.c:626:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
snprintf(key, sizeof(key), "%010lu", i + keyshift);
~~~~~^ ~~~~~~~~~~~~
%010u
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DataFrame_class.c -o DataFrame_class.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/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':
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1549:20: 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;
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:27: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:24: warning: too many arguments for format [-Wformat-extra-args]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^~~~~~
LLint_class.c:358:27: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:24: warning: too many arguments for format [-Wformat-extra-args]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^~~~~~
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)
~~~~~~~^~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c List_class.c -o List_class.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_S4Vectors.c -o R_init_S4Vectors.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rle_class.c -o Rle_class.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SEXP_utils.c -o SEXP_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleList_class.c -o SimpleList_class.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c character_utils.c -o character_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c eval_utils.c -o eval_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hash_utils.c -o hash_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c integer_utils.c -o integer_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c logical_utils.c -o logical_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c map_ranges_to_runs.c -o map_ranges_to_runs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c raw_utils.c -o raw_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c safe_arithm.c -o safe_arithm.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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)
^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c subsetting_utils.c -o subsetting_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vector_utils.c -o vector_utils.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def 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 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/libs/i386
** 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
converting help for package 'S4Vectors'
finding HTML links ... done
Annotated-class html
DataFrame-class html
DataFrame-combine html
DataFrame-comparison html
DataFrame-utils html
Factor-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/unfactor+2CFactor-method.html
FilterMatrix-class html
FilterRules-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/FilterRules.html
Hits-class html
Hits-comparison html
Hits-setops html
HitsList-class html
LLint-class html
List-class html
List-utils html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/revElements+2CList-method.html
Pairs-class html
RectangularData-class html
Rle-class html
Rle-runstat html
Rle-utils html
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S4Vectors-internals html
SimpleList-class html
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TransposedDataFrame-class html
Vector-class html
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Vector-comparison html
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Vector-merge html
Vector-setops html
aggregate-methods html
bindROWS html
character-utils html
expand-methods html
integer-utils html
isSorted html
shiftApply-methods html
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show-utils html
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splitAsList html
stack-methods html
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subsetting-utils html
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zip-methods html
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'S4Vectors' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_IntAEAE_toEnvir':
AEbufs.c:626:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
snprintf(key, sizeof(key), "%010lu", i + keyshift);
~~~~~^ ~~~~~~~~~~~~
%010I64u
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DataFrame_class.c -o DataFrame_class.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/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':
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1549:20: 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;
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:27: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:24: warning: too many arguments for format [-Wformat-extra-args]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^~~~~~
LLint_class.c:358:27: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:24: warning: too many arguments for format [-Wformat-extra-args]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^~~~~~
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)
~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c List_class.c -o List_class.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_S4Vectors.c -o R_init_S4Vectors.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rle_class.c -o Rle_class.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SEXP_utils.c -o SEXP_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleList_class.c -o SimpleList_class.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c character_utils.c -o character_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c eval_utils.c -o eval_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hash_utils.c -o hash_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c integer_utils.c -o integer_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c logical_utils.c -o logical_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c map_ranges_to_runs.c -o map_ranges_to_runs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c raw_utils.c -o raw_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c safe_arithm.c -o safe_arithm.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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)
^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c subsetting_utils.c -o subsetting_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vector_utils.c -o vector_utils.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.30.2.zip
* DONE (S4Vectors)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'S4Vectors' successfully unpacked and MD5 sums checked
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S4Vectors.Rcheck/tests_i386/run_unitTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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()
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
RUNIT TEST PROTOCOL -- Fri Oct 15 05:03:02 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
10.59 0.34 11.35
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S4Vectors.Rcheck/tests_x64/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-w64-mingw32/x64 (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()
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
RUNIT TEST PROTOCOL -- Fri Oct 15 05:03:13 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
10.23 0.25 10.46
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S4Vectors.Rcheck/examples_i386/S4Vectors-Ex.timings
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S4Vectors.Rcheck/examples_x64/S4Vectors-Ex.timings
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