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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:38:38 -0400 (Wed, 17 Oct 2018).
| Package 1305/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| S4Vectors 0.18.3 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: S4Vectors |
| Version: 0.18.3 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/S4Vectors_0.18.3.tar.gz && rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=S4Vectors.buildbin-libdir S4Vectors_0.18.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.18.3.zip && rm S4Vectors_0.18.3.tar.gz S4Vectors_0.18.3.zip |
| StartedAt: 2018-10-16 18:46:35 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 18:48:34 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 119.8 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/S4Vectors_0.18.3.tar.gz && rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=S4Vectors.buildbin-libdir S4Vectors_0.18.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.18.3.zip && rm S4Vectors_0.18.3.tar.gz S4Vectors_0.18.3.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 217k 100 217k 0 0 3165k 0 --:--:-- --:--:-- --:--:-- 3571k
install for i386
* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_increase_buflength':
AEbufs.c:31:2: warning: large integer implicitly truncated to unsigned type [-Woverflow]
return MAX_BUFLENGTH;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/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':
C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rinternals.h:1348:20: 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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'check_integer_runs':
Rle_class.c:218:20: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
*max_len_out_p = len_out;
^
Rle_class.c: In function '_construct_character_Rle':
Rle_class.c:509:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
len_out += len_in;
^
Rle_class.c:489:30: note: 'len_out' was declared here
unsigned long long int sum, len_out;
^
Rle_class.c: In function '_construct_raw_Rle':
Rle_class.c:606:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
len_out += len_in;
^
Rle_class.c:587:30: note: 'len_out' was declared here
unsigned long long int sum, len_out;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_32/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 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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/i386
** 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
converting help for package 'S4Vectors'
finding HTML links ... done
Annotated-class html
DataFrame-class html
DataTable-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/DataTable-class.Rd:57: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
FilterMatrix-class html
FilterRules-class html
Hits-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-class.Rd:81: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-class.Rd:177: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-class.Rd:188: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-class.Rd:283: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-class.Rd:286: file link 'Hits-examples' in package 'IRanges' does not exist and so has been treated as a topic
Hits-comparison html
Hits-setops html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-setops.Rd:47: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-setops.Rd:48: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Hits-setops.Rd:49: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
HitsList-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/HitsList-class.Rd:37: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/HitsList-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/HitsList-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/HitsList-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/HitsList-class.Rd:101: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/HitsList-class.Rd:103: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
LLint-class html
List-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:58: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:72: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:72: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:73: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:78: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:82: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:83: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:84: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:94: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:143: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:151: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:204: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:205: file link 'LogicalList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:205: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:206: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:207: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:207: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:257: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:260: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:260: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-class.Rd:261: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
List-utils html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:94: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:105: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:115: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:127: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:156: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:189: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:192: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:207: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:210: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/List-utils.Rd:214: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Pairs-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Pairs-class.Rd:46: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Pairs-class.Rd:47: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Pairs-class.Rd:105: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rle-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Rle-class.Rd:202: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Rle-class.Rd:221: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Rle-class.Rd:363: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
Rle-runstat html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Rle-runstat.Rd:95: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
Rle-utils html
S4Vectors-internals html
SimpleList-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/SimpleList-class.Rd:84: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/SimpleList-class.Rd:88: file link 'SimpleIntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Vector-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-class.Rd:208: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-class.Rd:216: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-class.Rd:333: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-class.Rd:348: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-class.Rd:349: file link 'XRaw' in package 'XVector' does not exist and so has been treated as a topic
Vector-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-comparison.Rd:292: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-comparison.Rd:325: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-comparison.Rd:341: missing file link 'IntegerRanges-comparison'
Vector-merge html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-merge.Rd:22: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-merge.Rd:22: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Vector-setops html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-setops.Rd:90: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-setops.Rd:91: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/Vector-setops.Rd:92: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
aggregate-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:38: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:38: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:42: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:44: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:45: file link 'SimpleAtomicList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:96: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/aggregate-methods.Rd:97: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
character-utils html
expand-methods html
integer-utils html
isSorted html
shiftApply-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/shiftApply-methods.Rd:44: file link 'window' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/shiftApply-methods.Rd:45: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
show-utils html
split-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/split-methods.Rd:47: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkBXqSg/R.INSTALLd1868803496/S4Vectors/man/split-methods.Rd:64: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
subsetting-utils html
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
In R CMD INSTALL
install for x64
* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/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':
C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rinternals.h:1348:20: 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
LLint_class.c: In function 'llints_summary':
LLint_class.c:791:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized]
res = _safe_llint_mult(res, in_elt);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_64/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 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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.18.3.zip
* DONE (S4Vectors)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'S4Vectors' successfully unpacked and MD5 sums checked
In R CMD INSTALL