bioconductor nightly build fails on Windows platform

[dimalvovs]

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### Running command:
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###   chmod a+r CoGAPS -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data CoGAPS
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* checking for file 'CoGAPS/DESCRIPTION' ... OK
* preparing 'CoGAPS':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'CoGAPS.Rmd' using rmarkdown
Data Model: Dense, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
-- Equilibration Phase --
10000 of 50000, Atoms: 68(A), 29(P), ChiSq: 329, Time: 00:00:00 / 00:00:00
20000 of 50000, Atoms: 74(A), 43(P), ChiSq: 161, Time: 00:00:00 / 00:00:00
30000 of 50000, Atoms: 84(A), 38(P), ChiSq: 141, Time: 00:00:00 / 00:00:00
40000 of 50000, Atoms: 80(A), 32(P), ChiSq: 143, Time: 00:00:01 / 00:00:02
50000 of 50000, Atoms: 81(A), 42(P), ChiSq: 117, Time: 00:00:01 / 00:00:02
-- Sampling Phase --
10000 of 50000, Atoms: 74(A), 43(P), ChiSq: 136, Time: 00:00:01 / 00:00:01
20000 of 50000, Atoms: 80(A), 37(P), ChiSq: 126, Time: 00:00:02 / 00:00:02
30000 of 50000, Atoms: 80(A), 41(P), ChiSq: 127, Time: 00:00:02 / 00:00:02
40000 of 50000, Atoms: 81(A), 38(P), ChiSq: 130, Time: 00:00:03 / 00:00:03
50000 of 50000, Atoms: 82(A), 44(P), ChiSq: 104, Time: 00:00:03 / 00:00:03
trying URL 'https://zenodo.org/record/7709664/files/inputdata.Rds?download=1'
Content type 'application/octet-stream' length 433262849 bytes (413.2 MB)
==================================================
downloaded 413.2 MB

Quitting from lines 235-240 [load single cell data from zenodo] (CoGAPS.Rmd)
Error: processing vignette 'CoGAPS.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building 'CoGAPS.Rmd'

SUMMARY: processing the following file failed:
  'CoGAPS.Rmd'

Error: Vignette re-building failed.
Execution halted

[dimalvovs]

This bug can be reproduced on the windows server platform outside bioconductor.

-- Equilibration Phase --
10000 of 50000, Atoms: 76(A), 31(P), ChiSq: 403, Time: 00:00:00 / 00:00:00
20000 of 50000, Atoms: 79(A), 37(P), ChiSq: 152, Time: 00:00:00 / 00:00:00
30000 of 50000, Atoms: 81(A), 33(P), ChiSq: 139, Time: 00:00:00 / 00:00:00
40000 of 50000, Atoms: 78(A), 38(P), ChiSq: 141, Time: 00:00:00 / 00:00:00
50000 of 50000, Atoms: 88(A), 38(P), ChiSq: 120, Time: 00:00:01 / 00:00:02
-- Sampling Phase --
10000 of 50000, Atoms: 83(A), 38(P), ChiSq: 112, Time: 00:00:01 / 00:00:01
20000 of 50000, Atoms: 86(A), 32(P), ChiSq: 115, Time: 00:00:01 / 00:00:01
30000 of 50000, Atoms: 78(A), 34(P), ChiSq: 182, Time: 00:00:02 / 00:00:02
40000 of 50000, Atoms: 80(A), 31(P), ChiSq: 120, Time: 00:00:02 / 00:00:02
50000 of 50000, Atoms: 86(A), 34(P), ChiSq: 145, Time: 00:00:02 / 00:00:02
trying URL 'https://zenodo.org/record/7709664/files/inputdata.Rds?download=1'
Content type 'application/octet-stream' length 433262849 bytes (413.2 MB)
==================================================
downloaded 413.2 MB

Quitting from lines 235-241 [load single cell data from zenodo] (CoGAPS.Rmd)
Error: processing vignette 'CoGAPS.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building 'CoGAPS.Rmd'

SUMMARY: processing the following file failed:
  'CoGAPS.Rmd'

Error: Vignette re-building failed.
Execution halted

C:\Users\lvovs\Documents\CoGAPS>

[dimalvovs]

To some reason, the file downloaded by a *nix system reads fine, but the file downloaded by a win-system can not be read (on any of the 2 platforms):

> proper <- readRDS('vignettes/inputdata_download.Rds')
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)

> corrupt <- readRDS('vignettes/inputdata_download 2.Rds')  # this one has been downloaded on win machine
Error in readRDS("vignettes/inputdata_download 2.Rds") : 
  error reading from connection

[dimalvovs]

ok, it works naturally if the proper parameter (mode='wb') added

> download.file(url,"inputdata_download_wb.Rds",mode='wb')

[dimalvovs]

other platforms are not affected by this change, closing the issue.

> url = "https://zenodo.org/record/7709664/files/inputdata.Rds"
> download.file(url,"inputdata_download.Rds", mode='wb')
trying URL 'https://zenodo.org/record/7709664/files/inputdata.Rds'
Content type 'application/octet-stream' length 433262849 bytes (413.2 MB)
==================================================
downloaded 413.2 MB

> pdac_data <- readRDS("inputdata_download.Rds")
> pdac_data
An object of class Seurat 
15184 features across 25442 samples within 2 assays 
Active assay: originalexp (15176 features, 2000 variable features)
 1 other assay present: CoGAPS
 5 dimensional reductions calculated: PCA, Aligned, UMAP, pca, umap

[dimalvovs]

it helped also on bioconductor

[dimalvovs]

the commit lacked same fix for the second download, and swapping knitr with markdown made vignette build fail silently

[dimalvovs]

moving this to #75 as these two are too much interconnected.