[R] Help with developing package DWLS
Bert Gunter
bgunter@4567 @end|ng |rom gm@||@com
Tue Jan 11 16:48:07 CET 2022
Andrew has already provided you a lot of help, but further posts should go
to r-package-devel, which is a mailing list specifically set up to provide
the sort of help you requested.
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Tue, Jan 11, 2022 at 12:10 AM Adriana Sistig <
adriana.sistig using icahn.mssm.edu> wrote:
> Hello,
>
> My name is Adriana Sistig and I am struggle to fix an ERROR and a few
> WARNING and NOTE message that I am getting from my package. I am new to
> CRAN packaging and am having some trouble finalizing my package.
>
> I do not have any ERRORS when I check using Mac but when checking via
> Windows and Debian I do. The current Status: 1 ERROR, 3 WARNINGs, 6 NOTEs —
> Pasted below for more information.
>
> GitHub link: https://github.com/sistia01/DWLS <
> https://github.com/sistia01/DWLS>
>
> Further information:
>
> > sessionInfo()
> R version 4.0.5 (2021-03-31)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Big Sur 10.16
>
> Matrix products: default
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] DWLS_0.1.0 Giotto_1.0.3 Biobase_2.50.0
> BiocGenerics_0.36.1
>
> loaded via a namespace (and not attached):
> [1] Seurat_4.0.5 Rtsne_0.15
> colorspace_2.0-2
> [4] deldir_1.0-6 class_7.3-19
> ellipsis_0.3.2
> [7] ggridges_0.5.3 XVector_0.30.0
> GenomicRanges_1.42.0
> [10] proxy_0.4-26 spatstat.data_2.1-0
> leiden_0.3.9
> [13] listenv_0.8.0 ggrepel_0.9.1 fansi_0.5.0
>
> [16] codetools_0.2-18 splines_4.0.5
> polyclip_1.10-0
> [19] jsonlite_1.7.2 ica_1.0-2
> cluster_2.1.2
> [22] png_0.1-7 uwot_0.1.11 shiny_1.7.1
>
> [25] sctransform_0.3.2 spatstat.sparse_2.0-0
> compiler_4.0.5
> [28] httr_1.4.2 SeuratObject_4.0.4
> Matrix_1.3-4
> [31] fastmap_1.1.0 lazyeval_0.2.2 cli_3.1.0
>
> [34] later_1.3.0 htmltools_0.5.2 tools_4.0.5
>
> [37] igraph_1.2.9 gtable_0.3.0 glue_1.6.0
>
> [40] GenomeInfoDbData_1.2.4 RANN_2.6.1
> reshape2_1.4.4
> [43] dplyr_1.0.7 Rcpp_1.0.7
> scattermore_0.7
> [46] vctrs_0.3.8 nlme_3.1-153
> lmtest_0.9-39
> [49] stringr_1.4.0 globals_0.14.0 mime_0.12
>
> [52] miniUI_0.1.1.1 lifecycle_1.0.1 irlba_2.3.5
>
> [55] goftest_1.2-3 future_1.23.0
> zlibbioc_1.36.0
> [58] MASS_7.3-54 zoo_1.8-9
> scales_1.1.1
> [61] MAST_1.16.0 spatstat.core_2.3-2
> promises_1.2.0.1
> [64] MatrixGenerics_1.2.1 spatstat.utils_2.2-0
> SummarizedExperiment_1.20.0
> [67] RColorBrewer_1.1-2 SingleCellExperiment_1.12.0
> reticulate_1.22
> [70] pbapply_1.5-0 gridExtra_2.3
> ggplot2_3.3.5
> [73] rpart_4.1-15 reshape_0.8.8
> stringi_1.7.6
> [76] S4Vectors_0.28.1 e1071_1.7-9
> GenomeInfoDb_1.26.7
> [79] rlang_0.4.12 pkgconfig_2.0.3
> matrixStats_0.61.0
> [82] bitops_1.0-7 lattice_0.20-45 ROCR_1.0-11
>
> [85] purrr_0.3.4 tensor_1.5
> patchwork_1.1.1
> [88] htmlwidgets_1.5.4 cowplot_1.1.1
> tidyselect_1.1.1
> [91] parallelly_1.29.0 RcppAnnoy_0.0.19 plyr_1.8.6
>
> [94] magrittr_2.0.1 R6_2.5.1
> IRanges_2.24.1
> [97] generics_0.1.1 DBI_1.1.1
> DelayedArray_0.16.3
> [100] mgcv_1.8-38 pillar_1.6.4
> fitdistrplus_1.1-6
> [103] survival_3.2-13 abind_1.4-5
> RCurl_1.98-1.5
> [106] tibble_3.1.6 future.apply_1.8.1
> crayon_1.4.2
> [109] KernSmooth_2.23-20 utf8_1.2.2
> spatstat.geom_2.3-0
> [112] plotly_4.10.0 grid_4.0.5
> data.table_1.14.2
> [115] digest_0.6.29 xtable_1.8-4 tidyr_1.1.4
>
> [118] httpuv_1.6.3 stats4_4.0.5
> munsell_0.5.0
> [121] viridisLite_0.4.0 quadprog_1.5-8
>
> > Sys.getlocale()
> [1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8”
>
> —————————————————
> * using log directory 'd:/RCompile/CRANguest/R-devel/DWLS.Rcheck'
> * using R Under development (unstable) (2022-01-09 r81462 ucrt)
> * using platform: x86_64-w64-mingw32 (64-bit)
> * using session charset: UTF-8
> * checking for file 'DWLS/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'DWLS' version '0.1.0'
> * package encoding: UTF-8
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: 'Adriana Sistig <adriana.sistig using icahn.mssm.edu>'
>
> New submission
>
> Possibly misspelled words in DESCRIPTION:
> DWLS (25:67, 32:42)
> Deconvolution (3:24)
> deconvolution (26:46)
> transcriptomic (10:51)
> * 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 whether package 'DWLS' can be installed ... OK
> * checking installed package size ... NOTE
> installed size is 66.4Mb
> sub-directories of 1Mb or more:
> data 66.3Mb
> * checking package directory ... OK
> * checking for future file timestamps ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... NOTE
> Non-standard files/directories found at top level:
> 'Reference_Manual_DWLS.md' 'Reference_Manual_Rd2md.md'
> * 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 loading without being on the library search path ... OK
> * checking use of S3 registration ... 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 ... [28s] NOTE
> DEAnalysisMAST: no visible binding for global variable
> 'Number.of.Cells'
> Undefined global functions or variables:
> Number.of.Cells
> * checking Rd files ... [1s] OK
> * checking Rd metadata ... OK
> * checking Rd line widths ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
> 'Sig' 'dataBulk' 'dataSC_1' 'dataSC_2' 'labels' 'trueLabels'
> Undocumented data sets:
> 'Sig' 'dataBulk' 'dataSC_1' 'dataSC_2' 'labels' 'trueLabels'
> All user-level objects in a package should have documentation entries.
> See chapter 'Writing R documentation files' in the 'Writing R
> Extensions' manual.
> * 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 LazyData ... WARNING
> LazyData DB of 66.3 MB without LazyDataCompression set
> See §1.1.6 of 'Writing R Extensions'
> * checking data for ASCII and uncompressed saves ... OK
> * checking R/sysdata.rda ... OK
> * checking examples ... [80s] NOTE
> Examples with CPU (user + system) or elapsed time > 10s
> user system elapsed
> stat.log2 50.87 11.58 62.45
> * checking for unstated dependencies in 'tests' ... OK
> * checking tests ... [9s] OK
> Running 'testthat.R' [9s]
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> LaTeX errors found:
> ! Package inputenc Error: Unicode character − (U+2212)
> (inputenc) not set up for use with LaTeX.
>
> See the inputenc package documentation for explanation.
> Type H <return> for immediate help.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> * checking for detritus in the temp directory ... NOTE
> Found the following files/directories:
> 'lastMiKTeXException'
> * DONE
> Status: 1 ERROR, 3 WARNINGs, 6 NOTEs
> ——————
> With regard to the NOTE about function DEAnalysisMAST —> I’m unsure about
> why this function in particular is throwing a note while other functions
> which use very similar code are not.
> I have tried a few different methods to create the pdf document of the
> manual but have not been able to succeed. I’m unsure of how to decipher the
> LaTeX Errors and have found from further research online that this may
> actually be quite an arduous task. I would greatly appreciate any help with
> this as it is not something that I have been able to solve on my own for
> the past few months. Please let me know if any further information is
> required. I thank you in advance for your help.
>
> Best,
> Adriana Sistig
>
>
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>
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