| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:50 -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 | ||||
|
To the developers/maintainers of the IRanges package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRanges.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 957/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IRanges 2.29.1 (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 | WARNINGS | OK | | ||||||||
| Package: IRanges |
| Version: 2.29.1 |
| Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir IRanges_2.29.1.tar.gz |
| StartedAt: 2022-03-17 21:16:05 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 21:18:53 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 168.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: IRanges_2.29.1.zip |
| PackageFileSize: 2.537 MiB |
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### Running command:
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### rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir IRanges_2.29.1.tar.gz
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* installing *source* package 'IRanges' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CompressedList_class.c -o CompressedList_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Grouping_class.c -o Grouping_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IPosRanges_comparison.c -o IPosRanges_comparison.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_class.c -o IRanges_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_constructor.c -o IRanges_constructor.o
IRanges_constructor.c: In function 'solve_range':
IRanges_constructor.c:43:22: warning: unknown conversion type character 'l' in format [-Wformat=]
"the 'width' (%lld) inferred from the "
^
IRanges_constructor.c:43:6: warning: too many arguments for format [-Wformat-extra-args]
"the 'width' (%lld) inferred from the "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:66:22: warning: unknown conversion type character 'l' in format [-Wformat=]
"the 'start' (%lld) inferred from the "
^
IRanges_constructor.c:66:6: warning: too many arguments for format [-Wformat-extra-args]
"the 'start' (%lld) inferred from the "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:86:20: warning: unknown conversion type character 'l' in format [-Wformat=]
"the 'end' (%lld) inferred from the "
^
IRanges_constructor.c:86:6: warning: too many arguments for format [-Wformat-extra-args]
"the 'end' (%lld) inferred from the "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:98:5: warning: unknown conversion type character 'l' in format [-Wformat=]
"the supplied 'width' (%d) doesn't match "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:100:27: note: format string is defined here
"'start' and 'end' (%lld)", width, tmp);
^
IRanges_constructor.c:98:5: warning: too many arguments for format [-Wformat-extra-args]
"the supplied 'width' (%d) doesn't match "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NCList.c -o NCList.o
NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
^~~~~~~~~~~~~
NCList.c: In function 'C_print_NCListAsINTSXP':
NCList.c:674:23: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=]
sprintf(format, "%c0%d%c", '%', max_digits, 'd');
^~
NCList.c:674:19: note: directive argument in the range [-2147483647, 2147483647]
sprintf(format, "%c0%d%c", '%', max_digits, 'd');
^~~~~~~~~
NCList.c:674:3: note: 'sprintf' output between 5 and 15 bytes into a destination of size 10
sprintf(format, "%c0%d%c", '%', max_digits, 'd');
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_IRanges.c -o R_init_IRanges.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Ranges_class.c -o Ranges_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RleViews_utils.c -o RleViews_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:579:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*out_ranges_are_tiles && x_end != cvg_len)
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c:495:21: note: 'x_end' was declared here
i, j, x_start, x_end, shift_elt, tmp;
^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'C_find_partition_overlaps':
extractListFragments.c:66:5: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(split_partitions_buf,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IntAE_get_nelt(split_partitions_buf),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
q_prev_end);
~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c inter_range_methods.c -o inter_range_methods.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.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/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
Creating a generic function for 'startsWith' from package 'base' in package 'IRanges'
Creating a generic function for 'endsWith' from package 'base' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a new generic function for 'windows' in package 'IRanges'
** help
*** installing help indices
converting help for package 'IRanges'
finding HTML links ... done
AtomicList-class html
finding level-2 HTML links ... done
AtomicList-utils html
CompressedHitsList-class html
CompressedList-class html
DataFrameList-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/ROWNAMES+2CDataFrameList-method.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/nrow+2CDataFrameList-method.html
Grouping-class html
Hits-class-leftovers html
IPos-class html
IPosRanges-class html
IPosRanges-comparison html
IRanges-class html
IRanges-constructor html
IRanges-internals html
IRanges-utils html
IRangesList-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/coerce+2CList+2CCompressedIRangesList-method.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/coerce+2CList+2CSimpleIRangesList-method.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/coerce+2CList+2CIRangesList-method.html
IntegerRanges-class html
IntegerRangesList-class html
MaskCollection-class html
NCList-class html
RangedSelection-class html
Rle-class-leftovers html
RleViews-class html
RleViewsList-class html
Vector-class-leftovers html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/window+3C-+2Cvector-method.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/window+3C-.vector.html
Views-class html
ViewsList-class html
coverage-methods html
extractList html
extractListFragments html
findOverlaps-methods html
inter-range-methods html
intra-range-methods html
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList'
Rd warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpeE8r4Y/R.INSTALLd6f06eb4b38/IRanges/man/intra-range-methods.Rd:297: missing link 'RangesList'
multisplit html
nearest-methods html
range-squeezers html
read.Mask html
reverse-methods html
seqapply html
setops-methods html
slice-methods html
view-summarization-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 'IRanges' as IRanges_2.29.1.zip
* DONE (IRanges)