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This page was generated on 2022-03-18 11:08:34 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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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 1693/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| S4Vectors 0.33.11 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: S4Vectors |
| Version: 0.33.11 |
| Command: rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=S4Vectors.buildbin-libdir S4Vectors_0.33.11.tar.gz |
| StartedAt: 2022-03-17 21:36:38 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 21:38:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 91.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: S4Vectors_0.33.11.zip |
| PackageFileSize: 2.295 MiB |
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### Running command:
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### rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=S4Vectors.buildbin-libdir S4Vectors_0.33.11.tar.gz
###
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* installing *source* package 'S4Vectors' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c DataFrame_class.c -o DataFrame_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Hits_class.c -o Hits_class.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rdefines.h:41,
from ../inst/include/S4Vectors_defines.h:18,
from S4Vectors.h:1,
from Hits_class.c:4:
Hits_class.c: In function 'Hits_new':
D:/biocbuild/bbs-3.15-bioc/R/include/Rinternals.h:877:20: 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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c List_class.c -o List_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_S4Vectors.c -o R_init_S4Vectors.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Rle_class.c -o Rle_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SEXP_utils.c -o SEXP_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SimpleList_class.c -o SimpleList_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c anyMissing.c -o anyMissing.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c character_utils.c -o character_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c eval_utils.c -o eval_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c hash_utils.c -o hash_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c integer_utils.c -o integer_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c logical_utils.c -o logical_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c map_ranges_to_runs.c -o map_ranges_to_runs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c raw_utils.c -o raw_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c safe_arithm.c -o safe_arithm.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c subsetting_utils.c -o subsetting_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/libs/x64
** 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: D:/biocbuild/bbs-3.15-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: D:/biocbuild/bbs-3.15-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: D:/biocbuild/bbs-3.15-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
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/summary+2CRle-method.html
S4Vectors-internals html
SimpleList-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/coerce+2Clist+2CList-method.html
TransposedDataFrame-class html
Vector-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/rename+2CVector-method.html
Vector-comparison html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/selfmatch+2Cfactor-method.html
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
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/shiftApply+2Cvector+2Cvector-method.html
show-utils html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/showAsCell+2Clist-method.html
splitAsList html
stack-methods html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/mstack+2Cvector-method.html
subsetting-utils html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/getListElement+2Clist-method.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/help/setListElement+2Clist-method.html
zip-methods html
** building package indices
** installing vignettes
** 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
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.33.11.zip
* DONE (S4Vectors)