Build/check report for BioC 3.24 - BIOCCHECK results for scPCA on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
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*
BIOCCHECK results for scPCA on nebbiolo2

To the developers/maintainers of the scPCA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scPCA.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: scPCA
Version: 1.27.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scPCA_1.27.0.tar.gz','quit-with-status'=TRUE)"
StartedAt: 2026-05-09 07:40:09 -0400 (Sat, 09 May 2026)
EndedAt: 2026-05-09 07:40:49 -0400 (Sat, 09 May 2026)
EllapsedTime: 40.0 seconds
RetCode: 0
Status: WARNINGS
CheckDir: None
Warnings: 1
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scPCA_1.27.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing scPCA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── scPCA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA
→ BiocVersion: 3.24
→ Package: scPCA
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scPCA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA
→ installDir: /tmp/Rtmpl8BLtz/file12cce92612e502
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scPCA ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.0.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (19%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:68: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:105: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:68: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:85: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:66: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:58: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:59: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:83: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:150: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:152: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:193: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:49: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:114: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:20: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:22: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:24: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:59: unknown macro '\insertAllCited'
* Checking for library/require of scPCA...
* Checking coding practice...
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/fitCPCA.R (line 63, column 19)
    • ...
    • R/spcaWrapper.R (line 65, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • safeColScale.R (line 53, column 36)
    • safeColScale.R (line 54, column 19)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • fitGrid() (R/fitGrid.R): 193 lines
    • ...
    • bpFitCPCA() (R/fitCPCA.R): 116 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:68: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:105: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:68: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:85: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:66: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:58: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:59: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:83: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:150: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:152: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:193: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:49: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:114: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:20: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:22: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:24: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:59: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:68: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:105: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:68: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:85: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:66: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:58: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:59: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:83: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:150: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:152: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:193: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:49: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:114: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:20: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:22: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:24: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:59: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitCPCA.Rd:68: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/bpFitGrid.Rd:105: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:68: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/checkArgs.Rd:85: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/cvSelectParams.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitCPCA.Rd:66: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/fitGrid.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:58: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:59: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:83: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:150: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:152: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/scPCA.Rd:193: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:49: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/selectParams.Rd:114: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:20: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:22: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:24: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:54: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpl8BLtz/file12cce91bfd97d5/scPCA/man/spcaWrapper.Rd:59: unknown macro '\insertAllCited'
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 21 lines (1%) are > 80 characters long.
  First few lines:
    • R/fitCPCA.R#L22 #' @param eigdecomp_tol A \code{numeric} ...
    • ...
    • vignettes/scpca_intro.Rmd#L584 [17](http://bioconductor.org/books/relea
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 619 lines (23%) are
not.
  First few lines:
    • R/checkArgs.R#L56 penalties, clust_m ...
    • ...
    • R/spcaWrapper.R#L109 return(loadings_mat) ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 8 NOTES
ℹ See the scPCA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.