Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:22:52 -0400 (Sat, 13 Apr 2019).
Package 1642/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
XVector 0.22.0 Hervé Pagès
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: XVector |
Version: 0.22.0 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XVector.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings XVector_0.22.0.tar.gz |
StartedAt: 2019-04-13 06:14:43 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 06:17:28 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 165.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: XVector.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XVector.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings XVector_0.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/XVector.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'XVector/DESCRIPTION' ... OK * this is package 'XVector' version '0.22.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'XVector' can be installed ... WARNING Found the following significant warnings: RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args] Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XDoubleViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XDoubleViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XDoubleViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XIntegerViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XIntegerViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XIntegerViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XRawList-comparison.Rd:106: missing file link 'Ranges-comparison' Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XVector-class.Rd:58: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XVector-class.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XVector-class.Rd:134: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:19: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:19: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:38: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:65: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/reverse-methods.Rd:48: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/slice-methods.Rd:14: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/slice-methods.Rd:53: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/XVector.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'BiocGenerics:::testPackage' 'IRanges:::new_Views' 'IRanges:::solveUserSEWForSingleSeq' 'S4Vectors:::anyMissing' 'S4Vectors:::prepare_objects_to_bind' 'S4Vectors:::setDefaultSlotValue' 'S4Vectors:::toNumSnippet' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'XRawList-comparison.Rd': '[IRanges]{Ranges-comparison}' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: 'RdaCollection' 'open_input_files' 'rdaPath' Undocumented S4 classes: 'RdaCollection' Undocumented S4 methods: generic '[[' and siglist 'RdaCollection' generic 'coerce' and siglist 'XVector,Rle' generic 'extractList' and siglist 'XVector,IntegerRanges' generic 'length' and siglist 'RdaCollection' generic 'names' and siglist 'RdaCollection' generic 'rdaPath' and siglist 'RdaCollection' generic 'relist' and siglist 'XVector,PartitioningByEnd' generic 'relistToClass' and siglist 'XVector' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/libs/i386/XVector.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'run_unitTests.R' OK ** running tests for arch 'x64' ... Running 'run_unitTests.R' OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/XVector.Rcheck/00check.log' for details.
XVector.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/XVector_0.22.0.tar.gz && rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XVector.buildbin-libdir XVector_0.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL XVector_0.22.0.zip && rm XVector_0.22.0.tar.gz XVector_0.22.0.zip ### ############################################################################## ############################################################################## % 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 67435 100 67435 0 0 1791k 0 --:--:-- --:--:-- --:--:-- 1995k install for i386 * installing *source* package 'XVector' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function 'RDS_read_character_vector': RDS_random_access.c:305:2: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^ RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c: In function 'RDS_read_atomic_vector': RDS_random_access.c:335:2: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^ RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c: In function 'RDS_read_list': RDS_random_access.c:379:2: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^ RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c: In function 'RDS_extract_subarray': RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable] SEXP subscript, ans; ^ RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable] SEXPTYPE x_type; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_XVector.c -o R_init_XVector.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SharedDouble_class.c -o SharedDouble_class.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SharedInteger_class.c -o SharedInteger_class.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript': SharedRaw_class.c:350:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable] SEXP dest, src_tag; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SharedVector_class.c -o SharedVector_class.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XRawList_comparison.c -o XRawList_comparison.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XVectorList_class.c -o XVectorList_class.o XVectorList_class.c: In function '_new_XRawList_from_CharAEAE': XVectorList_class.c:459:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized] _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XVector_class.c -o XVector_class.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c io_utils.c -o io_utils.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c slice_methods.c -o slice_methods.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vector_copy.c -o vector_copy.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c view_summarization_methods.c -o view_summarization_methods.o view_summarization_methods.c: In function 'get_which_min_from_Ints_holder': view_summarization_methods.c:219:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_min == NA_INTEGER || x < cur_min) { ^ view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder': view_summarization_methods.c:246:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_min == NA_INTEGER || x < cur_min) { ^ view_summarization_methods.c: In function 'get_which_max_from_Ints_holder': view_summarization_methods.c:269:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_max == NA_INTEGER || x > cur_max) { ^ view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder': view_summarization_methods.c:296:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_max == NA_INTEGER || x > cur_max) { ^ C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/XVector.buildbin-libdir/XVector/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'XVector' finding HTML links ... done OnDiskRaw-class html XDoubleViews-class html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XDoubleViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XDoubleViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XDoubleViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic XIntegerViews-class html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XIntegerViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XIntegerViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XIntegerViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic XRawList-class html XRawList-comparison html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XRawList-comparison.Rd:106: missing file link 'Ranges-comparison' XVector-class html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XVector-class.Rd:58: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XVector-class.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/XVector-class.Rd:134: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic XVector-internals html XVectorList-class html compact-methods html intra-range-methods html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:19: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:19: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:38: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/intra-range-methods.Rd:65: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic reverse-methods html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/reverse-methods.Rd:48: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic slice-methods html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/slice-methods.Rd:14: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpslXEAP/R.INSTALL1b1011273ab7/XVector/man/slice-methods.Rd:53: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic updateObject-methods html view-summarization-methods html ** building package indices ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'XVector' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function 'RDS_read_character_vector': RDS_random_access.c:305:2: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^ RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c: In function 'RDS_read_atomic_vector': RDS_random_access.c:335:2: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^ RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c: In function 'RDS_read_list': RDS_random_access.c:379:2: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^ RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args] RDS_random_access.c: In function 'RDS_extract_subarray': RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable] SEXP subscript, ans; ^ RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable] SEXPTYPE x_type; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_XVector.c -o R_init_XVector.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SharedDouble_class.c -o SharedDouble_class.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SharedInteger_class.c -o SharedInteger_class.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript': SharedRaw_class.c:350:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable] SEXP dest, src_tag; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SharedVector_class.c -o SharedVector_class.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XRawList_comparison.c -o XRawList_comparison.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XVectorList_class.c -o XVectorList_class.o XVectorList_class.c: In function '_new_XRawList_from_CharAEAE': XVectorList_class.c:459:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized] _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XVector_class.c -o XVector_class.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c io_utils.c -o io_utils.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c slice_methods.c -o slice_methods.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vector_copy.c -o vector_copy.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c view_summarization_methods.c -o view_summarization_methods.o view_summarization_methods.c: In function 'get_which_min_from_Ints_holder': view_summarization_methods.c:219:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_min == NA_INTEGER || x < cur_min) { ^ view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder': view_summarization_methods.c:246:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_min == NA_INTEGER || x < cur_min) { ^ view_summarization_methods.c: In function 'get_which_max_from_Ints_holder': view_summarization_methods.c:269:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_max == NA_INTEGER || x > cur_max) { ^ view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder': view_summarization_methods.c:296:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized] if (which_max == NA_INTEGER || x > cur_max) { ^ C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/XVector.buildbin-libdir/XVector/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'XVector' as XVector_0.22.0.zip * DONE (XVector) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'XVector' successfully unpacked and MD5 sums checked In R CMD INSTALL
XVector.Rcheck/tests_i386/run_unitTests.Rout R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("XVector") || stop("unable to load XVector package") Loading required package: XVector Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows [1] TRUE > XVector:::.test() RUNIT TEST PROTOCOL -- Sat Apr 13 06:17:20 2019 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : XVector RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 2.01 0.09 2.73 |
XVector.Rcheck/tests_x64/run_unitTests.Rout R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("XVector") || stop("unable to load XVector package") Loading required package: XVector Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows [1] TRUE > XVector:::.test() RUNIT TEST PROTOCOL -- Sat Apr 13 06:17:24 2019 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : XVector RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 3.10 0.14 3.23 |
XVector.Rcheck/examples_i386/XVector-Ex.timings
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XVector.Rcheck/examples_x64/XVector-Ex.timings
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