Error from runDE under Windows

[moldach]

I'm running into an issue when following the examples from the vignette for the runDE and runEA functions.

geo2kegg <- loadEData("geo2kegg")
geo2kegg <- maPreproc(geo2kegg[1:5])
geo2kegg[[1]]
se <- geo2kegg[[1]]
table(se$GROUP)
geo2kegg <- runDE(geo2kegg, de.method="limma", padj.method="flexible")

Error in .iter(exp.list, .de, ..., parallel = parallel) : 
  Error in as.vector(x, mode = "numeric") : 
  no method for coercing this S4 class to a vector

Similarly , I get an error with the runEA function:

library(EnrichmentBrowser)
kegg.gs <- getGenesets(org="hsa", db="kegg")
kegg.ora.res <- runEA(geo2kegg[[1]], method="ora", gs=kegg.gs, perm=0)

ora could not be evaluated on GSE1297
Error : subscript contains invalid names

Returning NULL

Not sure if it is best practice to open two separate issues for this; if so I apologize.

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] stringi_1.1.7

loaded via a namespace (and not attached):
 [1] matrixStats_0.54.0          lattice_0.20-35             IRanges_2.14.11             bitops_1.0-6               
 [5] GenomeInfoDb_1.16.0         grid_3.5.1                  stats4_3.5.1                zlibbioc_1.26.0            
 [9] XVector_0.20.0              S4Vectors_0.18.3            Matrix_1.2-14               BiocParallel_1.14.2        
[13] tools_3.5.1                 Biobase_2.40.0              RCurl_1.95-4.11             DelayedArray_0.6.6         
[17] yaml_2.2.0                  parallel_3.5.1              compiler_3.5.1              BiocGenerics_0.26.0        
[21] GenomicRanges_1.32.6        SummarizedExperiment_1.10.1 GenomeInfoDbData_1.1.0   

[lgeistlinger]

I cannot reproduce these errors here on a Mac and a Linux machine. It could be a windows-related problem, but unlikely to produce an error when executed as described in the vignette, building fine also under windows:

http://bioconductor.org/checkResults/release/bioc-LATEST/GSEABenchmarkeR/

Your sessionInfo looks unexpected, as I would assume to find GSEABenchmarkeR, EnrichmentBrowser, and their dependencies under other attached packages.

Can you confirm that the first error occurs when starting a fresh R session and executing:

library(GSEABenchmarkeR)
library(EnrichmentBrowser)

geo2kegg <- loadEData("geo2kegg")
geo2kegg <- maPreproc(geo2kegg[1:5])
geo2kegg <- runDE(geo2kegg, de.method="limma", padj.method="flexible")

The second error (runEA) then simply occurs due to the fact that runDE fails and required DE measures cannot be found during the ORA analysis.

[moldach]

The first error still occurs when starting a fresh R session and executing the code above. I have access to a Linux OS also so I ran the above and it works. So the problem is most certainly a Windows OS issue.

The msinfo32.exe for Windows is as follows:

OS Name Microsoft Windows 10 Pro
Version 10.0.17134 Build 17134
Other OS Description    Not Available
OS Manufacturer Microsoft Corporation
System Name HP_STUDENT_LAB
System Manufacturer Hewlett-Packard
System Model    HP Z230 SFF Workstation
System Type x64-based PC
System SKU  F1M17UT#ABA
Processor   Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz, 3601 Mhz, 4 Core(s), 8 Logical Processor(s)
BIOS Version/Date   Hewlett-Packard L51 v01.51, 4/13/2015
SMBIOS Version  2.7
Embedded Controller Version 255.255
BIOS Mode   UEFI
BaseBoard Manufacturer  Hewlett-Packard
BaseBoard Model Not Available
BaseBoard Name  Base Board
Platform Role   Workstation
Secure Boot State   Off
PCR7 Configuration  Elevation Required to View
Windows Directory   C:\WINDOWS
System Directory    C:\WINDOWS\system32
Boot Device \Device\HarddiskVolume2
Locale  Canada
Hardware Abstraction Layer  Version = "10.0.17134.285"
User Name   HP_student_lab\moldach
Time Zone   Eastern Daylight Time
Installed Physical Memory (RAM) 32.0 GB
Total Physical Memory   31.8 GB
Available Physical Memory   21.1 GB
Total Virtual Memory    63.8 GB
Available Virtual Memory    51.3 GB
Page File Space 32.0 GB
Page File   C:\pagefile.sys
Kernel DMA Protection   Off
Virtualization-based security   Not enabled
Device Encryption Support   Elevation Required to View
Hyper-V - VM Monitor Mode Extensions    Yes
Hyper-V - Second Level Address Translation Extensions   Yes
Hyper-V - Virtualization Enabled in Firmware    No
Hyper-V - Data Execution Protection Yes

[lgeistlinger]

Interesting. Apparently there are even differences between different windows systems with respect to parallelization in R. I'm looking into that as soon as I have access to a Windows machine. I'm renaming the issue for clarity.