Oliver Voogd
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/FLAMES |
| git_branch: RELEASE_3_16 |
| git_last_commit: 8e3c42d |
| git_last_commit_date: 2023-03-06 01:05:53 -0400 (Mon, 06 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:04 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 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. |
| Package 682/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FLAMES 1.4.3 (landing page) Oliver Voogd
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FLAMES |
| Version: 1.4.3 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL FLAMES |
| StartedAt: 2023-04-10 15:53:06 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 15:54:46 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 100.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL FLAMES
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppFunctions.cpp -o RcppFunctions.o
In file included from main-functions/../utility/fastq_utils.h:7,
from main-functions/match_cell_barcode.h:13,
from RcppFunctions.cpp:7:
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:185:12: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
185 | SCOPE int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:185:12: note: in definition of macro ‘__KSEQ_READ’
185 | SCOPE int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
| ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
12 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:171:13: warning: ‘void kseq_destroy(kseq_t*)’ defined but not used [-Wunused-function]
171 | SCOPE void kseq_destroy(kseq_t *ks) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:171:13: note: in definition of macro ‘__KSEQ_BASIC’
171 | SCOPE void kseq_destroy(kseq_t *ks) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
| ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
12 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:16: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
165 | SCOPE kseq_t *kseq_init(type_t fd) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:16: note: in definition of macro ‘__KSEQ_BASIC’
165 | SCOPE kseq_t *kseq_init(type_t fd) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
| ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
12 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/edit_dist.cpp -o utility/edit_dist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/fastq_utils.cpp -o utility/fastq_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam.c -o bam.o
bam.c: In function ‘bam_remove_B’:
bam.c:164:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
164 | for (k = 0; k < b->core.n_cigar; ++k)
| ^~~
bam.c:166:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
166 | if (k == b->core.n_cigar) return 0; // no 'B'
| ^~
bam.c:227:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
227 | for (k = 1; k < l; ++k)
| ^~~
bam.c:231:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
231 | for (k = i = 0; k < l; ++k)
| ^~~
bam.c:231:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
bam.c:234:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
234 | l = i;
| ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/ssw/ssw.c -o utility/ssw/ssw.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppFunctions.o RcppExports.o main-functions/match_cell_barcode.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-FLAMES/00new/FLAMES/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FLAMES)