| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:29 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 672/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FLAMES 1.5.1 (landing page) Voogd Oliver
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
| Package: FLAMES |
| Version: 1.5.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FLAMES_1.5.1.tar.gz |
| StartedAt: 2022-12-28 23:49:12 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:58:14 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 541.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: FLAMES.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FLAMES_1.5.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FLAMES.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FLAMES/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FLAMES' version '1.5.1'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 10.7Mb
sub-directories of 1Mb or more:
libs 9.3Mb
* 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
combine_sce: no visible global function definition for 'is'
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_plots: no visible binding for global variable 'gene_id'
sc_annotate_plots: no visible binding for global variable 'x'
sc_annotate_plots: no visible binding for global variable 'y'
sc_annotate_plots : plot_idx: no visible binding for global variable
'x'
sc_annotate_plots : plot_idx: no visible binding for global variable
'y'
sc_annotate_plots : plot_idx_impute: no visible binding for global
variable 'x'
sc_annotate_plots : 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-3.17-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)
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 nor [v]sprintf. 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 ... ERROR
Running examples in 'FLAMES-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parse_gff_tree
> ### Title: Parse Gff3 file
> ### Aliases: parse_gff_tree
>
> ### ** Examples
>
> temp_path <- tempfile()
> bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
> file_url <-
+ "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
> gff <- bfc[[names(BiocFileCache::bfcadd(bfc, "GFF", paste(file_url, "SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf", sep = "/")))]]
> parsed_gff <- parse_gff_tree(gff)
Warning in check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
+ "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/0/condabin/conda.bat" "create" "--yes" "--prefix" "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/FLAMES/1.5.1/flames_env" "python=3.7" "--quiet" "-c" "bioconda" "-c" "conda-forge"
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.11.2\FLAMES\1.5.1\flames_env
added / updated specs:
- python=3.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2022.12.7-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.40.0-hcfcfb64_0
openssl conda-forge/win-64::openssl-3.0.7-hcfcfb64_1
pip conda-forge/noarch::pip-22.3.1-pyhd8ed1ab_0
python conda-forge/win-64::python-3.7.12-h900ac77_100_cpython
setuptools conda-forge/noarch::setuptools-65.6.3-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.40.0-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
vc conda-forge/win-64::vc-14.3-h3d8a991_9
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.32.31332-h1d6e394_9
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/0/condabin/conda.bat" "install" "--yes" "--prefix" "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/FLAMES/1.5.1/flames_env" "python=3.7"
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.11.2\FLAMES\1.5.1\flames_env
added / updated specs:
- python=3.7
The following packages will be UPDATED:
python conda-forge::python-3.7.12-h900ac77_1~ --> pkgs/main::python-3.7.15-h6244533_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2022.10.11-haa95532_0
openssl conda-forge::openssl-3.0.7-hcfcfb64_1 --> pkgs/main::openssl-1.1.1s-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 22.11.1
Please update conda by running
$ conda update -n base -c defaults conda
+ "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/0/condabin/conda.bat" "install" "--yes" "--prefix" "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/FLAMES/1.5.1/flames_env" "-c" "bioconda" "-c" "conda-forge" "python=3.7" "python=3.7" "numpy=1.16.5" "editdistance=0.5.3" "scipy=1.2.0" "pysam=0.18.0"
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- pysam=0.18.0
Current channels:
- https://conda.anaconda.org/bioconda/win-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Error: one or more Python packages failed to install [error code 1]
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
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: 1 ERROR, 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FLAMES.Rcheck/00check.log'
for details.
FLAMES.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL FLAMES
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.17-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
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++17
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
185 | SCOPE int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: note: in definition of macro '__KSEQ_READ'
185 | SCOPE int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/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:15:1: note: in expansion of macro 'KSEQ_INIT'
15 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
171 | SCOPE void kseq_destroy(kseq_t *ks) \
| ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: note: in definition of macro '__KSEQ_BASIC'
171 | SCOPE void kseq_destroy(kseq_t *ks) \
| ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/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:15:1: note: in expansion of macro 'KSEQ_INIT'
15 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
165 | SCOPE kseq_t *kseq_init(type_t fd) \
| ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: note: in definition of macro '__KSEQ_BASIC'
165 | SCOPE kseq_t *kseq_init(type_t fd) \
| ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/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:15:1: note: in expansion of macro 'KSEQ_INIT'
15 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/bin.R: No such file or directory
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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:163:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
163 | for (k = 0; k < b->core.n_cigar; ++k)
| ^~~
bam.c:165:17: 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:226:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
226 | for (k = 1; k < l; ++k)
| ^~~
bam.c:230:25: 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:230:25: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
bam.c:233:33: 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-3.17-bioc/R/bin.R: No such file or directory
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.17-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-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
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> library(testthat)
> library(FLAMES)
>
> test_check("FLAMES")
Writing configuration parameters to: F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpGs16jh\file34b01c582c12/config_file_13488.json
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
17.26 1.23 18.53
FLAMES.Rcheck/FLAMES-Ex.timings
| name | user | system | elapsed | |
| annotation_to_fasta | 1.34 | 0.01 | 1.39 | |
| bulk_long_pipeline | 0.67 | 0.16 | 1.75 | |
| combine_sce | 1.50 | 0.19 | 1.69 | |
| create_config | 0.02 | 0.00 | 0.02 | |
| create_sce_from_dir | 0.17 | 0.01 | 2.66 | |
| create_se_from_dir | 0.54 | 0.14 | 1.03 | |
| find_barcode | 0.13 | 0.05 | 0.89 | |
| find_isoform | 0.61 | 0.12 | 0.99 | |
| get_GRangesList | 0.64 | 0.14 | 1.06 | |
| locate_minimap2_dir | 0.00 | 0.00 | 0.22 | |
| minimap2_align | 0.37 | 0.17 | 0.83 | |
| minimap2_realign | 0.61 | 0.05 | 0.98 | |