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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:21:29 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (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 | ||||
|
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 669/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FLAMES 1.2.2 (landing page) Voogd Oliver
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FLAMES |
| Version: 1.2.2 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FLAMES_1.2.2.tar.gz |
| StartedAt: 2022-10-19 00:15:25 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 00:23:00 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 455.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FLAMES.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FLAMES_1.2.2.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/FLAMES.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FLAMES/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FLAMES' version '1.2.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 'FLAMES' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
libs 7.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generate_sc_sce: no visible binding for global variable 'FSM_match'
sc_DTU_analysis: no visible global function definition for 'is'
sc_DTU_analysis: no visible binding for global variable 'FSM_match'
sc_DTU_analysis: no visible binding for global variable 'gene_name'
sc_DTU_analysis: no visible binding for global variable 'cell_id'
sc_DTU_analysis: no visible binding for global variable 'cnt'
sc_DTU_analysis: no visible binding for global variable 'tr_id'
sc_DTU_analysis : get_rm: no visible binding for global variable
'gene_name'
sc_DTU_analysis : get_rm: no visible binding for global variable 'l'
sc_annotate_umap: no visible binding for global variable 'FSM_match'
sc_annotate_umap: no visible binding for global variable 'gene_id'
sc_annotate_umap: no visible binding for global variable 'x'
sc_annotate_umap: no visible binding for global variable 'y'
sc_annotate_umap : plot_idx: no visible binding for global variable 'x'
sc_annotate_umap : plot_idx: no visible binding for global variable 'y'
sc_annotate_umap : plot_idx_impute: no visible binding for global
variable 'x'
sc_annotate_umap : plot_idx_impute: no visible binding for global
variable 'y'
Undefined global functions or variables:
FSM_match cell_id cnt gene_id gene_name is l tr_id x y
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/FLAMES/libs/x64/FLAMES.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'F:/biocbuild/bbs-3.15-bioc/meat/FLAMES.Rcheck/00check.log'
for details.
FLAMES.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FLAMES
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* 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)
| ^~~~~~~~~
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 main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.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 main-functions/merge_bulk.cpp -o main-functions/merge_bulk.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 utility/edit_dist.cpp -o utility/edit_dist.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 utility/fastq_utils.cpp -o utility/fastq_utils.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 utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
/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;
| ^
/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 utility/ssw/ssw.c -o utility/ssw/ssw.o
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/R/library/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
* DONE (FLAMES)
FLAMES.Rcheck/FLAMES-Ex.timings
| name | user | system | elapsed | |
| bulk_long_pipeline | 0.50 | 0.08 | 0.81 | |
| bulk_windows_pipeline_setup | 0.51 | 0.13 | 0.69 | |
| create_config | 0 | 0 | 0 | |
| create_sce_from_dir | 0.53 | 0.06 | 0.67 | |
| create_se_from_dir | 0.65 | 0.14 | 0.82 | |
| get_default_config_file | 0 | 0 | 0 | |
| gff3_to_bed12 | 0 | 0 | 0 | |
| merge_bulk_fastq | 0.83 | 0.09 | 0.95 | |
| merge_bulk_fastq_python | 0.38 | 0.19 | 0.61 | |
| parse_gff_tree | 0.25 | 0.03 | 0.44 | |
| parse_json_config | 0.01 | 0.00 | 0.01 | |
| samtools_as_bam | 1.24 | 0.05 | 2.24 | |
| samtools_sort_index | 0.75 | 0.11 | 1.09 | |
| sc_long_multisample_pipeline | 0.66 | 0.06 | 0.80 | |
| sc_long_pipeline | 0.78 | 0.11 | 1.05 | |
| sc_windows_pipeline_setup | 0.83 | 0.08 | 0.94 | |
| windows_pipeline_isoforms | 1.08 | 0.06 | 1.21 | |
| windows_pipeline_quantification | 1.14 | 0.09 | 1.30 | |