Question

no vignettes directory error during BiocCheck checking [SOLVED]

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waterincan • 0

@waterincan-21003

Last seen 5.5 years ago

Dear all, I'm trying to create a package and I have used usethis::use_vignette("my_vignette") to add a vignette. Unfortunately when I run the command BiocCheck(path_to_pkg) i have an error message stating:

[1] "No 'vignettes' directory."

although I indeed have a vignettes created by use_vignette command. I can't figure out why i have this message. (knitr is suggested in my DESCRIPTION file)

Thanks for any help.

Best.

BiocCheck • 1.4k views

ADD COMMENT • link 5.5 years ago waterincan • 0

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I'm currently unable to reproduce this. Could you provide the current directory structure of your package with system("tree <path to package>") or whatever call you prefer to list the directory structure as well as your systemInfo() so we know what OS you are using.

ADD REPLY • link 5.5 years ago shepherl 4.1k

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Hi Martin, Thank you very much for your reply. my Sys.info() gives me this

Sys.info()
                                      sysname                                       release 
                                      "Linux"                               "4.9.0-9-amd64" 
                                      version                                      nodename 
"#1 SMP Debian 4.9.168-1+deb9u2 (2019-05-13)"                                      "debian" 
                                      machine                                         login 
                                     "x86_64"                                     "apple" 
                                         user                                effective_user 
                                    "apple"                                     "apple"

ADD REPLY • link updated 5.5 years ago by Martin Morgan 25k • written 5.5 years ago by waterincan • 0

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for system(pathtopackage) it says sh: 1: /home/apple/R/x86_64-pc-linux-gnu-library/3.6/masan: Permission denied which is strange as it's in my home directory..

ADD REPLY • link 5.5 years ago waterincan • 0

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Can you please show the directory structure of your package. In the directory of your package you can type tree . You should get output something like the following:

lori@lori-HP-ZBook-15-G2:~/b/Rpacks/BiocFileCache(master)$ tree
.
├── DESCRIPTION
├── inst
│   └── schema
│       └── BiocFileCache.sql
├── man
│   ├── BiocFileCache-class.Rd
│   └── makeBiocFileCacheFromDataFrame.Rd
├── NAMESPACE
├── NEWS
├── R
│   ├── BiocFileCache-class.R
│   ├── httr.R
│   ├── makeBiocFileCacheFromDataFrame.R
│   ├── sql_migration.R
│   ├── sql.R
│   └── utilities.R
├── README.md
├── tests
│   ├── testthat
│   │   ├── test_BiocFileCache_class.R
│   │   ├── test_httr.R
│   │   ├── test_makeBiocFileCacheFromDataFrame.R
│   │   ├── test_sql_migration.R
│   │   ├── test_sql.R
│   │   └── test_utility.R
│   └── testthat.R
├── TODO.md
└── vignettes
    └── BiocFileCache.Rmd

7 directories, 22 files

So we can see the directory structure of your package.

ADD REPLY • link 5.5 years ago shepherl 4.1k

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tree
.
├── DESCRIPTION
├── devtools_history.R
├── inst
│   └── app
│       ├── server.R
│       └── ui.R
├── man
│   ├── masanDataInput.Rd
│   ├── masanData.Rd
│   ├── masanUI.Rd
│   └── shiny_app.Rd
├── masan.Rproj
├── NAMESPACE
├── R
│   ├── mod_ui_inputs.R
│   └── shiny_app.R
└── vignettes
    └── my_vignette.Rmd

ADD REPLY • link 5.5 years ago waterincan • 0

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Hi shepherl thank u very much. I was running bioccheck on the package path where it was installed (path given by .libPath) . I wasnt running it on the package where I was coding. I misunderstood the tutorial. Thank you very much

ADD REPLY • link 5.5 years ago waterincan • 0

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Hi shepherl thank u very much. I was running bioccheck on the package path where it was installed (path given by .libPath) . I wasnt running it on the package where I was coding. I misunderstood the tutorial. Thank you very much

ADD REPLY • link 5.5 years ago waterincan • 0

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Just glad you could figure it out and get it running. Let us know if you have any other issues.

ADD REPLY • link 5.5 years ago shepherl 4.1k

shepherl · Answer 1 · 2019-06-12

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waterincan • 0

@waterincan-21003

Last seen 5.5 years ago

tree

.
├── DESCRIPTION
├── devtools_history.R
├── inst
│   └── app
│       ├── server.R
│       └── ui.R
├── man
│   ├── masanDataInput.Rd
│   ├── masanData.Rd
│   ├── masanUI.Rd
│   └── shiny_app.Rd
├── masan.Rproj
├── NAMESPACE
├── R
│   ├── mod_ui_inputs.R
│   └── shiny_app.R
└── vignettes
    └── my_vignette.Rmd

ADD COMMENT • link updated 5.5 years ago by shepherl 4.1k • written 5.5 years ago by waterincan • 0

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In R could you do the following and show the results here

library(BiocCheck)
sessionInfo()

ADD REPLY • link 5.5 years ago shepherl 4.1k

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Also I know create_package and use_vignettes functions can change the R working directory from the original starting location. Are you sure you entered the correct path into the BiocCheck function.

Could you also please run and show the output of running the following in R:

dir( )
wd( )
BiocCheck(path to your package)

ADD REPLY • link 5.5 years ago shepherl 4.1k

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Thank you very much for your reply shepherl.

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

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=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
 [1] pd.hta.2.0_3.12.2   DBI_1.0.0          
 [3] RSQLite_2.1.1       masan_0.0.1        
 [5] oligo_1.48.0        Biostrings_2.52.0  
 [7] XVector_0.24.0      IRanges_2.18.1     
 [9] S4Vectors_0.22.0    Biobase_2.44.0     
[11] oligoClasses_1.46.0 BiocGenerics_0.30.0
[13] dplyr_0.8.1         shiny_1.3.2        
[15] usethis_1.5.0       devtools_2.0.2     
[17] BiocCheck_1.20.0   

loaded via a namespace (and not attached):
 [1] httr_1.4.0                  pkgload_1.0.2              
 [3] jsonlite_1.6                bit64_0.9-7                
 [5] splines_3.6.0               foreach_1.4.4              
 [7] assertthat_0.2.1            BiocManager_1.30.4         
 [9] blob_1.1.1                  RBGL_1.60.0                
[11] GenomeInfoDbData_1.2.1      remotes_2.0.4              
[13] sessioninfo_1.1.1           pillar_1.4.1               
[15] backports_1.1.4             lattice_0.20-38            
[17] glue_1.3.1                  RUnit_0.4.32               
[19] digest_0.6.19               GenomicRanges_1.36.0       
[21] promises_1.0.1              preprocessCore_1.46.0      
[23] htmltools_0.3.6             httpuv_1.5.1               
[25] Matrix_1.2-17               XML_3.98-1.20              
[27] pkgconfig_2.0.2             affxparser_1.56.0          
[29] zlibbioc_1.30.0             purrr_0.3.2                
[31] xtable_1.8-4                processx_3.3.1             
[33] stringdist_0.9.5.2          getopt_1.20.3              
[35] affyio_1.54.0               later_0.8.0                
[37] optparse_1.6.2              ff_2.2-14                  
[39] BiocParallel_1.18.0         tibble_2.1.3               
[41] biocViews_1.52.2            withr_2.1.2                
[43] SummarizedExperiment_1.14.0 cli_1.1.0                  
[45] magrittr_1.5                crayon_1.3.4               
[47] mime_0.7                    memoise_1.1.0              
[49] ps_1.3.0                    fs_1.3.1                   
[51] pkgbuild_1.0.3              graph_1.62.0               
[53] tools_3.6.0                 prettyunits_1.0.2          
[55] matrixStats_0.54.0          DelayedArray_0.10.0        
[57] callr_3.2.0                 compiler_3.6.0             
[59] GenomeInfoDb_1.20.0         rlang_0.3.4                
[61] grid_3.6.0                  RCurl_1.95-4.12            
[63] iterators_1.0.10            rstudioapi_0.10            
[65] bitops_1.0-6                testthat_2.1.1             
[67] codetools_0.2-16            R6_2.4.0                   
[69] knitr_1.23                  bit_1.1-14                 
[71] rprojroot_1.3-2             desc_1.2.0                 
[73] Rcpp_1.0.1                  tidyselect_0.2.5           
[75] xfun_0.7

ADD REPLY • link 5.5 years ago waterincan • 0