Comments (7)
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>
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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
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ok, it works naturally if the proper parameter (mode='wb') added
> download.file(url,"inputdata_download_wb.Rds",mode='wb')
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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
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it helped also on bioconductor
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the commit lacked same fix for the second download, and swapping knitr with markdown made vignette build fail silently
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moving this to #75 as these two are too much interconnected.
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Related Issues (20)
- Problem Installing Version 3.18.0 - clang: error: the clang compiler does not support '-march=native' HOT 2
- checkInputs Warning clarification
- Atoms and Patterns Stabilization
- 'Error in corcut' after full CoGAPS run HOT 3
- Package build fails on master
- Eliminate warnings during build HOT 4
- fix the check for semi supervised case
- SparseOptimization pattern discrepancy HOT 16
- Cache downloads for vignette
- enable sparse matrix support when input is object HOT 1
- limit number of cores for tests HOT 1
- Cpp tests
- Standard deviation when running distributed
- Vignettes fail on querying ENSEMBL
- Error when performing getPatternHallmarks: Error in 'collect()' HOT 9
- Replace Ensemble dependency and Add overrepresentation and enrichment tests for gene sets in patterns
- Confusion on the parallelization of R CoGAPS HOT 5
- GSEA algorithms for the function getPatternHallmarks HOT 9
- default number of patterns
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