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This page was generated on 2022-10-19 13:21:29 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

BUILD BIN results for FLAMES on palomino3


To the developers/maintainers of the FLAMES package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FLAMES.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 669/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FLAMES 1.2.2  (landing page)
Voogd Oliver
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/FLAMES
git_branch: RELEASE_3_15
git_last_commit: 2d5808d
git_last_commit_date: 2022-08-06 23:11:02 -0400 (Sat, 06 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FLAMES
Version: 1.2.2
Command: rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=FLAMES.buildbin-libdir FLAMES_1.2.2.tar.gz
StartedAt: 2022-10-19 05:53:32 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:55:09 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 97.2 seconds
RetCode: 0
Status:   OK  
PackageFile: FLAMES_1.2.2.zip
PackageFileSize: 4.98 MiB

Command output

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### Running command:
###
###   rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=FLAMES.buildbin-libdir FLAMES_1.2.2.tar.gz
###
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* installing *source* package 'FLAMES' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppFunctions.cpp -o RcppFunctions.o
In file included from main-functions/../utility/fastq_utils.h:9,
                 from main-functions/match_cell_barcode.h:16,
                 from RcppFunctions.cpp:7:
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  190 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: note: in definition of macro '__KSEQ_READ'
  190 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
  244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro 'KSEQ_INIT'
   15 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
  176 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: note: in definition of macro '__KSEQ_BASIC'
  176 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
  244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro 'KSEQ_INIT'
   15 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
  170 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: in definition of macro '__KSEQ_BASIC'
  170 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
  244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro 'KSEQ_INIT'
   15 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
/bin/sh: line 1: F:/biocbuild/bbs-3.15-bioc/R/bin.R: No such file or directory
gcc   -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam.c -o bam.o
bam.c: In function 'bam_remove_B':
bam.c:163:2: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  163 |  for (k = 0; k < b->core.n_cigar; ++k)
      |  ^~~
bam.c:165:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  165 |   if (k == b->core.n_cigar) return 0; // no 'B'
      |   ^~
bam.c:226:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  226 |   for (k = 1; k < l; ++k)
      |   ^~~
bam.c:230:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  230 |    for (k = i = 0; k < l; ++k)
      |    ^~~
bam.c:230:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
bam.c:233:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  233 |     l = i;
      |     ^
g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o main-functions/merge_bulk.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LF:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/meat/FLAMES.buildbin-libdir/00LOCK-FLAMES/00new/FLAMES/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 'FLAMES' as FLAMES_1.2.2.zip
* DONE (FLAMES)