| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:27 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 CellBarcode package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellBarcode.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 283/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellBarcode 1.7.0 (landing page) Wenjie Sun
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: CellBarcode |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CellBarcode_1.7.0.tar.gz |
| StartedAt: 2023-06-05 19:02:41 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 19:09:00 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 378.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellBarcode.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CellBarcode_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CellBarcode.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘CellBarcode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellBarcode’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CellBarcode’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 9.1Mb
sub-directories of 1Mb or more:
extdata 1.5Mb
libs 6.9Mb
* 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 loading without being on the library search path ... 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
bc_extract_10XscSeq: no visible binding for global variable
‘cell_barcode’
bc_extract_10XscSeq: no visible binding for global variable ‘umi’
bc_extract_10XscSeq: no visible binding for global variable
‘barcode_seq’
bc_2matrix,BarcodeObj: no visible binding for global variable
‘barcode_seq’
bc_cure_depth,BarcodeObj : <anonymous>: no visible binding for global
variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
variable ‘umi_seq’
bc_extract,character: no visible binding for global variable ‘i’
bc_extract,data.frame: no visible binding for global variable ‘umi_seq’
bc_extract,data.frame: no visible binding for global variable
‘barcode_seq’
bc_plot_seqQc,BarcodeQcSet: no visible binding for global variable
‘sample_name’
bc_subset,BarcodeObj : <anonymous>: no visible binding for global
variable ‘barcode_seq’
Undefined global functions or variables:
barcode_seq cell_barcode i sample_name umi umi_seq
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
‘Barcode_in_10X_scRNASeq.Rmd’ using ‘UTF-8’... OK
‘UMI_VDJ_Barcode.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/CellBarcode.Rcheck/00check.log’
for details.
CellBarcode.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CellBarcode
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘CellBarcode’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -fPIC -g -O2 -c lib_10X_barcode.cpp -o lib_10X_barcode.o
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string.hpp:23,
from lib_10X_barcode.cpp:8:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/classification.hpp:15,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/trim.hpp:23,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string.hpp:19,
from lib_10X_barcode.cpp:8:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -fPIC -g -O2 -c lib_clustering.cpp -o lib_clustering.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -fPIC -g -O2 -c lib_read_seq.cpp -o lib_read_seq.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o CellBarcode.so RcppExports.o lib_10X_barcode.o lib_clustering.o lib_read_seq.o -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-CellBarcode/00new/CellBarcode/libs
** R
** data
** 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 (CellBarcode)
CellBarcode.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.
> library(testthat)
> library(CellBarcode)
>
> test_check("CellBarcode")
------------
bc_cure_depth: isUpdate is FALSE, use messyBc as input.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is FALSE, use messyBc as input.
------------
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 35 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 35 ]
>
> proc.time()
user system elapsed
15.147 1.215 16.376
CellBarcode.Rcheck/CellBarcode-Ex.timings
| name | user | system | elapsed | |
| BarcodeObj | 0.479 | 0.008 | 0.488 | |
| bc_2df | 0.016 | 0.000 | 0.016 | |
| bc_auto_cutoff | 0.003 | 0.000 | 0.004 | |
| bc_barcodes | 0.001 | 0.000 | 0.002 | |
| bc_cleanBc | 0.002 | 0.004 | 0.005 | |
| bc_cure_cluster | 0.062 | 0.008 | 0.069 | |
| bc_cure_depth | 0.028 | 0.000 | 0.028 | |
| bc_cure_umi | 0.018 | 0.000 | 0.018 | |
| bc_extract | 0.378 | 0.024 | 0.404 | |
| bc_extract_10X_scSeq | 0.007 | 0.000 | 0.008 | |
| bc_messyBc | 0.006 | 0.000 | 0.006 | |
| bc_meta | 0.005 | 0.000 | 0.005 | |
| bc_names | 0.002 | 0.000 | 0.002 | |
| bc_plot_mutual | 0.511 | 0.004 | 0.516 | |
| bc_plot_pair | 0.293 | 0.008 | 0.302 | |
| bc_plot_single | 1.507 | 0.092 | 1.602 | |
| bc_seq_filter | 0.458 | 0.012 | 0.472 | |
| bc_seq_qc | 2.626 | 0.055 | 2.686 | |
| bc_splitVDJ | 1.224 | 0.020 | 1.246 | |
| bc_subset | 0.143 | 0.000 | 0.141 | |
| bc_summary_barcode | 0.619 | 0.000 | 0.619 | |
| bc_summary_seqQc | 4.824 | 0.128 | 4.973 | |
| format | 0.004 | 0.000 | 0.004 | |
| show | 0.003 | 0.000 | 0.003 | |
| subset | 3.863 | 0.048 | 3.919 | |