Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 297/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellBarcode 1.12.0  (landing page)
Wenjie Sun
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CellBarcode
git_branch: RELEASE_3_20
git_last_commit: d63a174
git_last_commit_date: 2024-10-29 11:06:31 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CellBarcode on merida1

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.
- 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.

raw results


Summary

Package: CellBarcode
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-12-20 00:51:32 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:00:24 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 532.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CellBarcode.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CellBarcode.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellBarcode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellBarcode’ version ‘1.12.0’
* 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 code 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_sc_fastq: no visible binding for global variable
  ‘cell_barcode’
bc_extract_sc_fastq: no visible binding for global variable ‘umi’
bc_extract_sc_fastq: no visible binding for global variable
  ‘barcode_seq’
process_sc_list: no visible binding for global variable ‘cell_barcode’
process_sc_list: no visible binding for global variable ‘umi’
process_sc_list: 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,data.frame: no visible binding for global variable ‘umi_seq’
bc_extract,data.frame: no visible binding for global variable
  ‘barcode_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘barcode_read_count’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘raw_read_count’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘umi_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘barcode_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘cell_barcode’
bc_plot_count,BarcodeObj: no visible binding for global variable ‘V1’
bc_plot_count,BarcodeObj: no visible binding for global variable ‘x’
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:
  V1 barcode_read_count barcode_seq cell_barcode raw_read_count
  sample_name umi umi_seq x
* 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 8.007  0.125   8.206
subset           7.970  0.085   8.184
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/CellBarcode.Rcheck/00check.log’
for details.


Installation output

CellBarcode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CellBarcode
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib_10X_barcode.cpp -o lib_10X_barcode.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib_clustering.cpp -o lib_clustering.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib_read_seq.cpp -o lib_read_seq.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/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)

Tests output

CellBarcode.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 TRUE, update the cleanBc.
------------
------------
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, saveRDS, setdiff, 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 37 ]

══ 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 37 ]
> 
> proc.time()
   user  system elapsed 
 26.187   2.056  28.909 

Example timings

CellBarcode.Rcheck/CellBarcode-Ex.timings

nameusersystemelapsed
BarcodeObj0.9350.0640.999
bc_2df0.0340.0060.049
bc_auto_cutoff0.0070.0030.011
bc_barcodes0.0020.0020.005
bc_cleanBc0.0140.0080.021
bc_create_BarcodeObj0.0220.0030.026
bc_cure_cluster0.1220.0080.127
bc_cure_depth0.0540.0060.057
bc_cure_umi0.0340.0050.037
bc_extract0.7830.0590.832
bc_extract_sc_sam0.2360.0170.237
bc_messyBc0.0140.0070.019
bc_meta0.0090.0040.012
bc_names0.0020.0030.005
bc_plot_count2.1720.0262.243
bc_plot_mutual0.5960.0080.647
bc_plot_pair0.5070.0200.537
bc_plot_single1.1240.1501.288
bc_seq_filter1.2270.7111.956
bc_seq_qc4.0440.1684.306
bc_splitVDJ2.1670.0222.202
bc_subset0.2480.0100.256
bc_summary_barcode0.9550.0170.934
bc_summary_seqQc8.0070.1258.206
format0.0060.0020.009
show0.0060.0020.008
subset7.9700.0858.184