Closed hpages closed 3 years ago
I can't reproduce this.
> library(BiocCheck)
> BiocCheck("MatrixQCvis_0.99.3.tar.gz")
This is BiocCheck version 1.27.13. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Registered S3 method overwritten by 'dendextend':
method from
rev.hclust vegan
Registered S3 method overwritten by 'seriation':
method from
reorder.hclust vegan
* Checking if other packages can import this one...
* ERROR: Packages providing 1 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
package::object in function()
plotly::partial_bundle in distServer ()
* Checking to see if we understand object initialization...
* 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...
Package version 0.99.3; pre-release
* Checking R Version dependency...
* Checking package size...
* Checking individual file sizes...
* WARNING: The following files are over 5MB in size:
'inst/doc/MatrixQCvis.html'
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Sequencing, Coverage
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import ComplexHeatmap in DESCRIPTION as well as
NAMESPACE.
* Checking .Rbuildignore...
* Checking vignette directory...
This is a software package
* Checking library calls...
* Checking for library/require of MatrixQCvis...
* Checking coding practice...
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpPg9nMI/file448052c7e334/MatrixQCvis/tests/testthat.R'
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
Error in params$missingValue :
object of type 'closure' is not subsettable
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.......................................................
* NOTE: Recommended function length <= 50 lines.
There are 25 functions > 50 lines.
The longest 5 functions are:
.initialize_server() (R/shinyQC.R, line 218): 527 lines
maServer() (R/module_values.R, line 757): 158 lines
_anonymous_.762() (R/module_values.R, line 762): 151 lines
shinyQC() (R/shinyQC.R, line 68): 124 lines
maxQuant() (R/conversion.R, line 112): 93 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
8% of man pages use one of these cases.
Found in the following files:
biocrates.Rd
maxQuant.Rd
shinyQC.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 32 lines (0%) are > 80 characters
long.
First 6 lines:
R/conversion.R:156 rD$Unique_razor_sequence_coverage <- xls[, "...
R/module_global.R:121 condition = "input.tabs == 'Dimension Red...
R/module_global.R:172 conditionalPanel("output.missingVals == 'TRUE...
R/shinyQC.R:134 $(".main-sidebar .sidebar").css({"p...
R/shinyQC.R:379 "It seems you have applied a batch corr...
R/shinyQC.R:380 "Please make sure to assess the existen...
* NOTE: Consider multiples of 4 spaces for line indents, 95
lines(1%) are not.
First 6 lines:
R/module_values.R:76 selected = "boxplot")),
man/create_boxplot.Rd:8 se,
man/create_boxplot.Rd:9 orderCategory = colnames(colData(se)),
man/create_boxplot.Rd:10 title = "",
man/create_boxplot.Rd:11 log2 = TRUE,
man/create_boxplot.Rd:12 violin = FALSE
See http://bioconductor.org/developers/how-to/coding-style/
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...
* 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...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 2
WARNING count: 2
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "Packages providing 1 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail."
[2] "Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags."
$warning
[1] "The following files are over 5MB in size: 'inst/doc/MatrixQCvis.html'"
[2] "Import ComplexHeatmap in DESCRIPTION as well as NAMESPACE."
$note
[1] "Consider adding these automatically suggested biocViews: Sequencing, Coverage"
[2] "License 'GPL (>= 3)' unknown; licenses cannot restrict use"
[3] "Recommended function length <= 50 lines."
[4] "Usage of dontrun{} / donttest{} found in man page examples."
[5] "Consider shorter lines; 32 lines (0%) are > 80 characters long."
[6] "Consider multiples of 4 spaces for line indents, 95 lines(1%) are not."
[7] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials). Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"
> sessionInfo()
R Under development (unstable) (2021-04-09 r80152)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /home/shepherd/R-Installs/bin/R-devel/lib/libRblas.so
LAPACK: /home/shepherd/R-Installs/bin/R-devel/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] MatrixQCvis_0.99.3 shiny_1.6.0
[3] plotly_4.9.3 ggplot2_3.3.3
[5] SummarizedExperiment_1.21.3 Biobase_2.51.0
[7] GenomicRanges_1.43.4 GenomeInfoDb_1.27.11
[9] IRanges_2.25.9 S4Vectors_0.29.15
[11] BiocGenerics_0.37.2 MatrixGenerics_1.3.1
[13] matrixStats_0.58.0 BiocCheck_1.27.13
[15] praise_1.0.0 BiocManager_1.30.12
loaded via a namespace (and not attached):
[1] backports_1.2.1 circlize_0.4.12 Hmisc_4.5-0
[4] proDA_1.5.0 plyr_1.8.6 gmm_1.6-6
[7] lazyeval_0.2.2 shinydashboard_0.7.1 splines_4.1.0
[10] digest_0.6.27 foreach_1.5.1 htmltools_0.5.1.1
[13] viridis_0.6.0 fansi_0.4.2 magrittr_2.0.1
[16] checkmate_2.0.0 xlsx_0.6.5 cluster_2.1.2
[19] doParallel_1.0.16 limma_3.47.12 ComplexHeatmap_2.7.9
[22] imputeLCMD_2.0 sandwich_3.0-0 askpass_1.1
[25] jpeg_0.1-8.1 colorspace_2.0-0 xfun_0.22
[28] dplyr_1.0.5 crayon_1.4.1 RCurl_1.98-1.3
[31] jsonlite_1.7.2 graph_1.69.0 impute_1.65.0
[34] survival_3.2-10 zoo_1.8-9 iterators_1.0.13
[37] ape_5.4-1 glue_1.4.2 registry_0.5-1
[40] gtable_0.3.0 zlibbioc_1.37.0 XVector_0.31.1
[43] webshot_0.5.2 UpSetR_1.4.0 GetoptLong_1.0.5
[46] DelayedArray_0.17.10 shape_1.4.5 scales_1.1.1
[49] vsn_3.59.1 mvtnorm_1.1-1 DBI_1.1.1
[52] Rcpp_1.0.6 viridisLite_0.4.0 xtable_1.8-4
[55] htmlTable_2.1.0 clue_0.3-59 reticulate_1.18
[58] foreign_0.8-81 preprocessCore_1.53.2 Formula_1.2-4
[61] MsCoreUtils_1.3.3 umap_0.2.7.0 htmlwidgets_1.5.3
[64] httr_1.4.2 getopt_1.20.3 RColorBrewer_1.1-2
[67] ellipsis_0.3.1 rJava_0.9-13 pkgconfig_2.0.3
[70] XML_3.99-0.6 nnet_7.3-15 utf8_1.2.1
[73] tidyselect_1.1.0 shinyhelper_0.3.2 rlang_0.4.10
[76] later_1.1.0.1 munsell_0.5.0 biocViews_1.59.3
[79] tools_4.1.0 generics_0.1.0 evaluate_0.14
[82] stringr_1.4.0 fastmap_1.1.0 yaml_2.2.1
[85] heatmaply_1.2.1 knitr_1.32 purrr_0.3.4
[88] dendextend_1.14.0 RBGL_1.67.0 nlme_3.1-152
[91] mime_0.10 compiler_4.1.0 rstudioapi_0.13
[94] curl_4.3 png_0.1-7 affyio_1.61.0
[97] tibble_3.1.1 stringi_1.5.3 RSpectra_0.16-0
[100] lattice_0.20-41 Matrix_1.3-2 permute_0.9-5
[103] shinyjs_2.0.0 vegan_2.5-7 tmvtnorm_1.4-10
[106] vctrs_0.3.7 stringdist_0.9.6.3 pillar_1.6.0
[109] norm_1.0-9.5 lifecycle_1.0.0 RUnit_0.4.32
[112] optparse_1.6.6 GlobalOptions_0.1.2 data.table_1.14.0
[115] bitops_1.0-6 seriation_1.2-9 httpuv_1.5.5
[118] affy_1.69.1 R6_2.5.0 latticeExtra_0.6-29
[121] pcaMethods_1.83.0 TSP_1.1-10 promises_1.2.0.1
[124] gridExtra_2.3 codetools_0.2-18 MASS_7.3-53.1
[127] assertthat_0.2.1 xlsxjars_0.6.1 openssl_1.4.3
[130] rjson_0.2.20 withr_2.4.2 GenomeInfoDbData_1.2.4
[133] mgcv_1.8-35 grid_4.1.0 rpart_4.1-15
[136] tidyr_1.1.3 rmarkdown_2.7 Cairo_1.5-12.2
[139] Rtsne_0.15 base64enc_0.1-3
>
I see it in your output ;-)
This error happens because the old code was checking every folder including inst/
(there's bad code in the inst
folder but I'm not sure if that is something we want to check).
I've updated the code to only look at R files and vignettes.
packageVersion("BiocCheck")
#> [1] '1.29.14'
BiocCheck::BiocCheck("~/gh/MatrixQCvis")
This is BiocCheck version 1.29.14. BiocCheck is a work in progress. Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking version number validity...
* Checking R Version dependency...
* Checking package size...
Skipped... only checked on source tarball
* 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...
* NOTE: Consider adding these automatically suggested biocViews: Sequencing, Coverage
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of MatrixQCvis...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
suppressWarnings() in R/tab_values.R (line 203, column 9)
suppressWarnings() in R/tab_values.R (line 815, column 9)
suppressWarnings() in R/tab_values.R (line 1066, column 14)
* Checking function lengths........................................................
* NOTE: Recommended function length <= 50 lines.
There are 26 functions > 50 lines.
The longest 5 functions are:
.initialize_server() (R/shinyQC.R, line 216): 536 lines
maServer() (R/module_values.R, line 821): 170 lines
_anonymous_.826() (R/module_values.R, line 826): 163 lines
shinyQC() (R/shinyQC.R, line 63): 123 lines
maxQuant() (R/conversion.R, line 115): 94 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
10% of man pages use one of these cases.
Found in the following files:
biocrates.Rd
maxQuant.Rd
shinyQC.Rd
volcanoPlot.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source...
* NOTE: Consider shorter lines; 44 lines (0%) are > 80 characters long.
First 6 lines:
R/conversion.R:90 #' function from the `openxlsx` package (e.g. specifying the sheet name or index
R/conversion.R:159 rD$Unique_razor_sequence_coverage <- xls[, "Unique...razor.sequence.coverage...."]
R/landingPage.R:60 shiny::showNotification("invalid SummarizedExperiment supplied",
R/module_dimensionreduction.R:78 plotly::plotlyOutput(outputId = ns("plot"), height = "auto") %>%
R/module_dimensionreduction.R:200 plotly::plotlyOutput(outputId = ns("plot"), height = "auto") %>%
R/module_dimensionreduction.R:258 plotly::plotlyOutput(outputId = ns("plot"), height = "auto") %>%
* NOTE: Consider multiples of 4 spaces for line indents, 81 lines(1%) are not.
First 6 lines:
R/module_values.R:85 selected = "boxplot")),
man/batchCorrectionAssay.Rd:9 se,
man/batchCorrectionAssay.Rd:10 method = c("none", "removeBatchEffect (limma)"),
man/batchCorrectionAssay.Rd:11 batchColumn = colnames(colData(se))
man/create_boxplot.Rd:8 se,
man/create_boxplot.Rd:9 orderCategory = colnames(colData(se)),
See http://bioconductor.org/developers/how-to/coding-style/
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...
* 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...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 8
For detailed information about these checks, see the BiocCheck vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
$error
character(0)
$warning
character(0)
$note
[1] "Consider adding these automatically suggested biocViews: Sequencing, Coverage"
[2] "License 'GPL (>= 3)' unknown; licenses cannot restrict use"
[3] "Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)"
[4] "Recommended function length <= 50 lines."
[5] "Usage of dontrun{} / donttest{} found in man page examples."
[6] "Consider shorter lines; 44 lines (0%) are > 80 characters long."
[7] "Consider multiples of 4 spaces for line indents, 81 lines(1%) are not."
[8] "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials). Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"
Created on 2021-08-13 by the reprex package (v2.0.1)
Running
BiocCheck()
on the MatrixQCvis package (https://github.com/tnaake/MatrixQCvis) produces "object of type 'closure' is not subsettable" errors:sessionInfo():