Wenjie Sun
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/CellBarcode |
| git_branch: RELEASE_3_17 |
| git_last_commit: 53dc39e |
| git_last_commit_date: 2023-04-25 11:34:35 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 287/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellBarcode 1.6.0 (landing page) Wenjie Sun
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the CellBarcode package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CellBarcode |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellBarcode_1.6.0.tar.gz |
| StartedAt: 2023-10-17 07:59:44 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 08:06:37 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 413.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellBarcode.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellBarcode_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CellBarcode.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellBarcode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellBarcode’ version ‘1.6.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bc_summary_seqQc 4.886 0.078 7.572
subset 3.502 0.063 5.442
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CellBarcode.Rcheck/00check.log’
for details.
CellBarcode.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CellBarcode ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘CellBarcode’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib_10X_barcode.cpp -o lib_10X_barcode.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib_clustering.cpp -o lib_clustering.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib_read_seq.cpp -o lib_read_seq.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CellBarcode.so RcppExports.o lib_10X_barcode.o lib_clustering.o lib_read_seq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-BarcodeObj.R:119:3', 'test-describ.R:51:3',
'test-qc.R:17:3'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 35 ]
>
> proc.time()
user system elapsed
13.414 0.651 21.539
CellBarcode.Rcheck/CellBarcode-Ex.timings
| name | user | system | elapsed | |
| BarcodeObj | 0.579 | 0.046 | 0.938 | |
| bc_2df | 0.016 | 0.003 | 0.027 | |
| bc_auto_cutoff | 0.004 | 0.001 | 0.010 | |
| bc_barcodes | 0.001 | 0.001 | 0.002 | |
| bc_cleanBc | 0.005 | 0.003 | 0.015 | |
| bc_cure_cluster | 0.051 | 0.004 | 0.081 | |
| bc_cure_depth | 0.024 | 0.003 | 0.042 | |
| bc_cure_umi | 0.016 | 0.002 | 0.029 | |
| bc_extract | 0.528 | 0.039 | 0.872 | |
| bc_extract_10X_scSeq | 0.006 | 0.002 | 0.016 | |
| bc_messyBc | 0.006 | 0.002 | 0.012 | |
| bc_meta | 0.005 | 0.001 | 0.010 | |
| bc_names | 0.001 | 0.001 | 0.002 | |
| bc_plot_mutual | 0.338 | 0.009 | 0.528 | |
| bc_plot_pair | 0.244 | 0.008 | 0.380 | |
| bc_plot_single | 0.578 | 0.039 | 0.962 | |
| bc_seq_filter | 0.557 | 0.033 | 0.906 | |
| bc_seq_qc | 2.425 | 0.053 | 3.762 | |
| bc_splitVDJ | 1.155 | 0.018 | 1.805 | |
| bc_subset | 0.132 | 0.005 | 0.213 | |
| bc_summary_barcode | 0.544 | 0.009 | 0.848 | |
| bc_summary_seqQc | 4.886 | 0.078 | 7.572 | |
| format | 0.003 | 0.001 | 0.006 | |
| show | 0.003 | 0.001 | 0.007 | |
| subset | 3.502 | 0.063 | 5.442 | |