Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/S4Vectors |
| Branch: RELEASE_3_6 |
| Last Commit: 00fec03 |
| Last Changed Date: 2017-10-30 12:40:15 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:24:16 -0400 (Thu, 12 Apr 2018).
| Package 1238/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| S4Vectors 0.16.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: S4Vectors |
| Version: 0.16.0 |
| Command: rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=S4Vectors.buildbin-libdir --merge-multiarch S4Vectors_0.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.16.0.zip && rm S4Vectors_0.16.0.tar.gz S4Vectors_0.16.0.zip |
| StartedAt: 2018-04-11 18:14:03 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:16:01 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 117.7 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=S4Vectors.buildbin-libdir --merge-multiarch S4Vectors_0.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.16.0.zip && rm S4Vectors_0.16.0.tar.gz S4Vectors_0.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 204k 100 204k 0 0 7890k 0 --:--:-- --:--:-- --:--:-- 9274k
install for i386
* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-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˜1.6-B/R/include/Rinternals.h:1214:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define defineVar Rf_defineVar
^
Hits_class.c:218:12: note: 'revmap' was declared here
SEXP ans, revmap, symbol;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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:317:3: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:317:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_32/bin/g++ -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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/i386
** R
** inst
** preparing package for lazy loading
in method for 'extractROWS' with signature '"array","RangesNSBS"': no definition for class "RangesNSBS"
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-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/DataTable-class.Rd:57: missing file link 'RangedData'
FilterMatrix-class html
FilterRules-class html
Hits-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Hits-class.Rd:81: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Hits-class.Rd:254: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Hits-class.Rd:257: missing file link 'Hits-examples'
Hits-comparison html
Hits-setops html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Hits-setops.Rd:47: missing file link 'union'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Hits-setops.Rd:48: missing file link 'intersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Hits-setops.Rd:49: missing file link 'setdiff'
HitsList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/HitsList-class.Rd:37: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/HitsList-class.Rd:38: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/HitsList-class.Rd:47: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/HitsList-class.Rd:70: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/HitsList-class.Rd:101: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/HitsList-class.Rd:103: missing file link 'RangesList'
LLint-class html
List-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:57: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:71: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:71: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:72: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:73: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:77: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:81: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:82: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:82: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:92: missing file link 'CompressedList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:141: missing file link 'CompressedList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:149: missing file link 'CompressedList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:202: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:203: missing file link 'LogicalList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:203: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:204: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:205: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:205: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:255: missing file link 'CompressedList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:258: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:258: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-class.Rd:259: missing file link 'IRanges'
List-utils html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:106: missing file link 'sapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:117: missing file link 'Reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:127: missing file link 'rbind'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:139: missing file link 'sapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:168: missing file link 'Reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:201: missing file link 'Reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:204: missing file link 'within'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:219: missing file link 'Reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:222: missing file link 'within'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/List-utils.Rd:226: missing file link 'rbind'
Pairs-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Pairs-class.Rd:49: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Pairs-class.Rd:50: missing file link 'findOverlapPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Pairs-class.Rd:108: missing file link 'findOverlapPairs'
Rle-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Rle-class.Rd:209: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Rle-class.Rd:366: missing file link 'aggregate'
Rle-runstat html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Rle-runstat.Rd:95: missing file link 'RleList-class'
Rle-utils html
S4Vectors-internals html
SimpleList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/SimpleList-class.Rd:88: missing file link 'CompressedList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/SimpleList-class.Rd:92: missing file link 'SimpleIntegerList'
Vector-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-class.Rd:243: missing file link 'CompressedList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-class.Rd:258: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-class.Rd:259: missing file link 'XRaw'
Vector-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-comparison.Rd:283: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-comparison.Rd:315: missing file link 'Ranges'
Vector-merge html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-merge.Rd:22: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-merge.Rd:22: missing file link 'DNAStringSet'
Vector-setops html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-setops.Rd:90: missing file link 'union'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-setops.Rd:91: missing file link 'intersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/Vector-setops.Rd:92: missing file link 'setdiff'
aggregate-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:38: missing file link 'end'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:38: missing file link 'width'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:42: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:43: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:44: missing file link 'SimpleAtomicList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:95: missing file link 'end'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/aggregate-methods.Rd:96: missing file link 'width'
character-utils html
expand-methods html
isSorted html
shiftApply-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/shiftApply-methods.Rd:44: missing file link 'window'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/shiftApply-methods.Rd:45: missing file link 'aggregate'
show-utils html
split-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/split-methods.Rd:47: missing file link 'splitAsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaY5qPN/R.INSTALLe702191188/S4Vectors/man/split-methods.Rd:64: missing file link 'splitAsList'
subsetting-utils html
zip-methods html
** building package indices
** installing vignettes
'RleTricks.Rnw' using 'UTF-8'
'S4QuickOverview.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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-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˜1.6-B/R/include/Rinternals.h:1214:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define defineVar Rf_defineVar
^
Hits_class.c:218:12: note: 'revmap' was declared here
SEXP ans, revmap, symbol;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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:317:3: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:317:3: warning: too many arguments for format [-Wformat-extra-args]
LLint_class.c: In function 'llints_summary':
LLint_class.c:750:9: 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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_64/bin/g++ -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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.16.0.zip
* DONE (S4Vectors)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'S4Vectors' successfully unpacked and MD5 sums checked
In R CMD INSTALL