Install problem

[dg13]

Hi Ramon,
Thanks for the great package and dataset - I'm getting an error trying to install:

devtools::install_github("massonix/HCATonsilData", build_vignettes = TRUE) Downloading GitHub repo massonix/HCATonsilData@HEAD ✔ checking for file ‘/private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/Rtmp5lxC9o/remotes9c5c5c953635/massonix-HCATonsilData-59187d4/DESCRIPTION’ (411ms) ─ preparing ‘HCATonsilData’: ✔ checking DESCRIPTION meta-information ... ─ installing the package to build vignettes ----------------------------------- ─ installing *source* package ‘HCATonsilData’ ... ** using staged installation ** R Error in parse(outFile) : /private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/RtmpG6nFZf/Rbuild9c7a4c45bdde/HCATonsilData/R/HCATonsilData.R:52:33: unexpected input 51: "pca", "harmony", "umap") 52: filePaths <- sapply(suffixes, \ ^ ERROR: unable to collate and parse R files for package ‘HCATonsilData’ ─ removing ‘/private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/RtmpG6nFZf/Rinst9c7a76b460f0/HCATonsilData’ ----------------------------------- ERROR: package installation failed Error: Failed to install 'HCATonsilData' from GitHub: System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines): E> ** R E> Error in parse(outFile) : E> /private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/RtmpG6nFZf/Rbuild9c7a4c45bdde/HCATonsilData/R/HCATonsilData.R:52:33: unexpected input E> 51: "pca", "harmony", "umap") E> 52: filePaths <- sapply(suffixes, \ E> ^ E> ERROR: unable to collate and parse R files for package ‘HCATonsilData’ E> * removing ‘/private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/RtmpG6nFZf/Rinst9c7a76b460f0/HCATonsilData’ E> ----------------------------------- E> ERROR: package installation failed

Here's my sessionInfo()

`sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS: /usr/local/Cellar/r/4.0.3/lib/R/lib/libRblas.dylib
LAPACK: /usr/local/Cellar/r/4.0.3/lib/R/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
[1] ps_1.5.0 prettyunits_1.1.1 withr_2.5.0 rprojroot_2.0.2
[5] crayon_1.5.1 R6_2.5.1 lifecycle_1.0.1 magrittr_2.0.3
[9] rlang_1.0.3 cachem_1.0.6 cli_3.3.0 curl_4.3.2
[13] remotes_2.4.2 fs_1.5.2 callr_3.7.0 ellipsis_0.3.2
[17] devtools_2.4.3 tools_4.0.3 glue_1.6.2 purrr_0.3.4
[21] pkgload_1.3.0 fastmap_1.1.0 compiler_4.0.3 processx_3.5.2
[25] pkgbuild_1.2.0 sessioninfo_1.2.2 memoise_2.0.1 usethis_2.1.6`

Any ideas?
Thanks
Dan

[federicomarini]

Hi Dan,
Can you try to replicate the error also on a most recent version of R and Bioconductor?
Since this is going to be submitted to Bioc, we are ensuring that the latest environment is as reproducible as we can.

Alternatively: can you try to install without building the vignette?

HTH,
Federico

[dg13]

Thanks! Here's what I get with build_vignettes=FALSE

`devtools::install_github("massonix/HCATonsilData", build_vignettes = FALSE)
Downloading GitHub repo massonix/HCATonsilData@HEAD
✔ checking for file ‘/private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/Rtmp5lxC9o/remotes9c5c25f96624/massonix-HCATonsilData-59187d4/DESCRIPTION’ (841ms)
─ preparing ‘HCATonsilData’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘HCATonsilData_0.0.0.9000.tar.gz’

Installing package into ‘/usr/local/lib/R/4.0/site-library’
(as ‘lib’ is unspecified)

• installing source package ‘HCATonsilData’ ...
  ** using staged installation
  ** R
  Error in parse(outFile) :
  /private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/Rtmpi6qqlb/R.INSTALLa876344774ab/HCATonsilData/R/HCATonsilData.R:52:33: unexpected input
  51: "pca", "harmony", "umap")
  52: filePaths <- sapply(suffixes,
  ^
  ERROR: unable to collate and parse R files for package ‘HCATonsilData’
• removing ‘/usr/local/lib/R/4.0/site-library/HCATonsilData’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T//Rtmp5lxC9o/file9c5c18a0d8f6/HCATonsilData_0.`

I'll have a go with a more up to date version of R and Bioconductor

[dg13]

I've updated to R 4.2.1 and I can now install with build_vignettes = FALSE! However, build_vignettes = TRUE hangs on me for > 1hr. Is that expected?

[federicomarini]

The vignette in its current form does include some long-running computations, so, yes, as of now it is the expected behavior.
We are considering leaving some unEVALuated chunks to make it slimmer.
Or well, alternatively, the user can just opt to not build it, and in that case it should be reasonably fast.

Thanks for trying it out in the recent setup!
Federico

[dg13]

OK great I'll leave it going over night and see what happens - thanks for the quick responses and making the data so easy to access!

[dg13]

Hi again,
last night I tried installing with vignettes, but got a (new) error

`devtools::install_github("massonix/HCATonsilData", build_vignettes = TRUE,force=TRUE)
Downloading GitHub repo massonix/HCATonsilData@HEAD
✔ checking for file ‘/private/var/folders/yh/ls2hbq6j7039g1b2ldmrkvbh0000gp/T/RtmpkDjnKz/remotes12ad0556e27b4/massonix-HCATonsilData-59187d4/DESCRIPTION’ (639ms)
─ preparing ‘HCATonsilData’:
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
E creating vignettes (1m 0.1s)
--- re-building ‘HCATonsilData.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

   colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
   colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
   colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
   colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
   colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
   colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
   colWeightedMeans, colWeightedMedians, colWeightedSds,
   colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
   rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
   rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
   rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
   rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
   rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
   rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
   rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

   IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

   Filter, Find, Map, Position, Reduce, anyDuplicated, append,
   as.data.frame, basename, cbind, colnames, dirname, do.call,
   duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
   lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
   pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
   tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

   I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

   Vignettes contain introductory material; view with
   'browseVignettes()'. To cite Bioconductor, see
   'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

   rowMedians

The following objects are masked from 'package:matrixStats':

   anyMissing, rowMedians

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

   cache

Quitting from lines 117-119 (HCATonsilData.Rmd)
Error: processing vignette 'HCATonsilData.Rmd' failed with diagnostics:
HDF5. File accessibility. Unable to open file.
--- failed re-building ‘HCATonsilData.Rmd’

SUMMARY: processing the following file failed:
‘HCATonsilData.Rmd’

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'HCATonsilData' from GitHub:
! System command 'R' failed`

Here's my sessionInfo
`sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin21.5.0 (64-bit)
Running under: macOS Monterey 12.4

Matrix products: default
BLAS: /usr/local/Cellar/openblas/0.3.20/lib/libopenblasp-r0.3.20.dylib
LAPACK: /usr/local/Cellar/r/4.2.1/lib/R/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] BiocManager_1.30.18

loaded via a namespace (and not attached):
[1] ps_1.7.1 prettyunits_1.1.1 withr_2.5.0 rprojroot_2.0.3
[5] crayon_1.5.1 R6_2.5.1 lifecycle_1.0.1 magrittr_2.0.3
[9] rlang_1.0.3 cachem_1.0.6 cli_3.3.0 curl_4.3.2
[13] remotes_2.4.2 fs_1.5.2 callr_3.7.0 ellipsis_0.3.2
[17] devtools_2.4.3 tools_4.2.1 glue_1.6.2 purrr_0.3.4
[21] pkgload_1.3.0 fastmap_1.1.0 compiler_4.2.1 processx_3.6.1
[25] pkgbuild_1.3.1 sessioninfo_1.2.2 memoise_2.0.1 usethis_2.1.6`

Can anyone make sense of this?
Thanks
Dan

[federicomarini]

The culprit is

Quitting from lines 117-119 (HCATonsilData.Rmd)
Error: processing vignette 'HCATonsilData.Rmd' failed with diagnostics:
HDF5. File accessibility. Unable to open file.

Looks like it cannot open the hdf5 file as expected.

Can you try to run the lines of the vignette in an interactive session?