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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scRecover_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scRecover ────────────────────────────────────────────────────────
✔ Package installed successfully
── scRecover session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGhRnsP/file12d728371a9ce7/scRecover
→ BiocVersion: 3.24
→ Package: scRecover
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scRecover.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpGhRnsP/file12d728371a9ce7/scRecover
→ installDir: /tmp/RtmpGhRnsP/file12d72816c79954
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scRecover ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Normalization,
Clustering
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (6%).
* 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...
* Checking for library/require of scRecover...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/imputation_model.R (line 4, column 8)
    • ...
    • R/imputation_model.R (line 358, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/get_mix_parameters.R (line 67, column 9)
    • ...
    • print() in R/write_count.R (line 20, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/calculate_weight.R (line 4, column 9)
    • ...
    • R/write_count.R (line 10, column 15)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • countsSampling.R (line 63, column 90)
    • ...
    • scRecover.R (line 74, column 69)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/imputation_model.R (line 174, column 3)
  • set.seed() in R/imputation_model.R (line 238, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/estDropoutNum.R (line 97, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • scRecover() (R/scRecover.R): 279 lines
    • ...
    • mleZINB() (R/mleZINB.R): 82 lines
* Checking man page documentation...
Registered S3 method overwritten by 'gamlss':
  method   from
  print.ri bit 
* 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; 129 lines (7%) are > 80 characters long.
  First few lines:
    • R/countsSampling.R#L3 #' This function is used to downsample t ...
    • ...
    • vignettes/scRecover.Rmd#L312 MOE Key Laboratory of Bioinformatics; Bi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/scRecover.R#L161 print("Rmagic is not available now...") ...
    • R/scRecover.R#L163 counts_MAGIC <- counts ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 514 lines (29%) are
not.
  First few lines:
    • R/countsSampling.R#L52 # Handle SingleCellExperiment ...
    • ...
    • vignettes/scRecover.Rmd#L21 comment = "#>" ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 12 NOTES
ℹ See the scRecover.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.