Search
Question: Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
0
gravatar for Jenny Drnevich
20 months ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:

Hi all,

So I've somehow gotten my R installation in a bad state. I had been using R 3.3.2 / BioC 3.4, last installed/updated likely in late November and everything was fine. I decided to upgrade packages again using biocLite(); I thought I had closed all R other sessions and didn't have any packages loaded when I did this, but I must not have because I got lots of warnings about "unable to write to folder XXX", then the packages were unable to load. I've had this happen before and the fix has been to go manually delete the package folders from my R library, then reinstall. This seemed to work, but the next time I loaded affycoretools, I got a warning message about "vfs customization not available on this platform. Ignoring value: vfs = unix-none". I shrugged and went on. The first problem I noticed was when I tried to call plotPCA on a matrix and got the error "Error in (function (classes, fdef, mtable)  :  unable to find an inherited method for function 'plotPCA' for signature '"matrix"'. The same code was working fine with affycoretools 1.46.1 but after upgrading to 1.46.3 it wasn't. I don't mean to pick on affycoretools (sorry, Jim!) because I get the same warning about "vfs customization" when installing .db annotation packages (full output below), so it must be system wide.

I've even gone as far as deleting all versions of R from my computer (I only had 3.3.2 and Devel),  all personal libraries, deleting my Rtools installation, everything from my path variable and even Rstudio. I also googled ""vfs customization not available on this platform" but didn't find anything useful. The outputs below are from a fresh install of R 3.3.2. Anybody have any idea of what is wrong and how I can fix it?

Thanks,

Jenny

# The first part of the output is here, but the full output makes the message too long, so I'll post the rest separately...

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

> source("https://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
  'lib = "C:/Program Files/R/R-3.3.2/library"' is not writable
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/BiocInstaller_1.24.0.zip'
Content type 'application/zip' length 126079 bytes (123 KB)
downloaded 123 KB

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘digest’, ‘memoise’, ‘Rcpp’, ‘BH’, ‘plogr’, ‘BiocGenerics’, ‘S4Vectors’, ‘DBI’, ‘RSQLite’

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.11 0.6.12              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.11.zip'
Content type 'application/zip' length 168720 bytes (164 KB)
downloaded 164 KB

#lines deleted

package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
installation path not writeable, unable to update packages: Matrix, mgcv, nlme,
  survival
Old packages: 'digest'
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.11 0.6.12              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.11.zip'
Content type 'application/zip' length 168720 bytes (164 KB)
downloaded 164 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
> biocLite("affycoretools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘affycoretools’
also installing the dependencies ‘httpuv’, ‘sourcetools’, ‘backports’, 

# lines deleted

package ‘affycoretools’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
installing the source packages ‘GO.db’, ‘PFAM.db’

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/GO.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31897756 bytes (30.4 MB)
downloaded 30.4 MB

# lines deleted

* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (GO.db)
#lines deleted 

> library(affycoretools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

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

Welcome to Bioconductor

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

Warning messages:
1: vfs customization not available on this platform. Ignoring value: vfs = unix-none
2: vfs customization not available on this platform. Ignoring value: vfs = unix-none
3: vfs customization not available on this platform. Ignoring value: vfs = unix-none
> setwd("D:/Statistics/Dobrucki")
> library(limma)

Attaching package: 'limma'

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

    plotMA

> targets <- readTargets("Targets.txt")
> 
> targets$trt <- targets$Cy5
> targets$trt[targets$Cy5 == "cont"] <- targets$Cy3[targets$Cy5 == "cont"]
> f <- function(x) as.numeric(x$Flags> -99)
> 
> 
> #Read in the data, using the median foreground and background values
> 
> RG <- read.maimages(targets$FileName,source="genepix.median",names=targets$Label,wt.fun=f,
+                 annotation=c("Block", "Row", "Column", "ID", "Name", "ControlType","GeneName"))
Read 1A_588_0452.gpr 
Read 1B_606_0462.gpr 
Read 1C_571_0473.gpr 
Read 1D_576_0475.gpr 
Read 2A_571_0427.gpr 
Read 2B_560_0435.gpr 
Read 2C_526_0433.gpr 
Read 2D_536_0448.gpr 
> spottypes <- readSpotTypes()
> RG$genes$Status <- controlStatus(spottypes,RG)
Matching patterns for: ControlType 
Found 45220 cDNA 
Found 1224 pos 
Found 153 neg 
Found 823 ignore 
Setting attributes: values Color 
> RG.nobg <- backgroundCorrect(RG,method="none")
> 
> targ2 <- data.frame(Sample = c(targets$cy5samp, targets$cy3samp), 
+                     group = c(targets$Cy5, targets$Cy3), FileName = rep(targets$FileName,2),
+                     Array = rep(targets$array, 2), Slide = rep(targets$slide,2),
+                     Dye = rep(c("R","G"), each = nrow(targets)),
+                     Pair = rep(targets$pair, 2))

> #add in label
> 
> targ2$Label <- paste(targ2$group, targ2$Pair, sep = ".")
> RG.quant <- RG.MA(normalizeBetweenArrays(RG.nobg,method="quantile"))
> plotPCA(log2(cbind(RG.quant$R,RG.quant$G)),groups=as.numeric(factor(targ2$group)),
+         groupnames=levels(factor(targ2$group)),addtext=targ2$Pair)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'plotPCA' for signature '"matrix"'
> affycoretools::plotPCA(log2(cbind(RG.quant$R,RG.quant$G)),groups=as.numeric(factor(targ2$group)),
+         groupnames=levels(factor(targ2$group)),addtext=targ2$Pair)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'plotPCA' for signature '"matrix"'
> biocLite("MmAgilentDesign026655.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) 'MmAgilentDesign026655.db'
also installing the dependency 'org.Mm.eg.db'

installing the source packages 'org.Mm.eg.db', 'MmAgilentDesign026655.db'

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/org.Mm.eg.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 63616251 bytes (60.7 MB)
downloaded 60.7 MB

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1479706 bytes (1.4 MB)
downloaded 1.4 MB

* installing *source* package 'org.Mm.eg.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (org.Mm.eg.db)
* installing *source* package 'MmAgilentDesign026655.db' ...
** R
** inst
** preparing package for lazy loading
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (MmAgilentDesign026655.db)

# the rest of the code I'll post in the thread. 

ADD COMMENTlink modified 20 months ago by James W. MacDonald47k • written 20 months ago by Jenny Drnevich1.9k
0
gravatar for Jenny Drnevich
20 months ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
#Here's the  rest of the output


The downloaded source packages are in
        'C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages'
installation path not writeable, unable to update packages: Matrix, mgcv, nlme,
  survival
Old packages: 'digest'
Update all/some/none? [a/s/n]: n
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

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

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

other attached packages:
[1] limma_3.30.9         affycoretools_1.46.3 Biobase_2.34.0      
[4] BiocGenerics_0.20.0  BiocInstaller_1.24.0

loaded via a namespace (and not attached):
  [1] Category_2.40.0               bitops_1.0-6                 
  [3] RColorBrewer_1.1-2            httr_1.2.1                   
  [5] GenomeInfoDb_1.10.2           gcrma_2.46.0                 
  [7] tools_3.3.2                   backports_1.0.5              
  [9] affyio_1.44.0                 R6_2.2.0                     
 [11] KernSmooth_2.23-15            rpart_4.1-10                 
 [13] Hmisc_4.0-2                   DBI_0.5-1                    
 [15] lazyeval_0.2.0                colorspace_1.3-2             
 [17] nnet_7.3-12                   gridExtra_2.2.1              
 [19] GGally_1.3.0                  DESeq2_1.14.1                
 [21] bit_1.1-12                    preprocessCore_1.36.0        
 [23] graph_1.52.0                  htmlTable_1.9                
 [25] rtracklayer_1.34.1            ggbio_1.22.3                 
 [27] caTools_1.17.1                scales_0.4.1                 
 [29] checkmate_1.8.2               affy_1.52.0                  
 [31] genefilter_1.56.0             RBGL_1.50.0                  
 [33] stringr_1.1.0                 digest_0.6.11                
 [35] Rsamtools_1.26.1              foreign_0.8-67               
 [37] R.utils_2.5.0                 AnnotationForge_1.16.0       
 [39] XVector_0.14.0                base64enc_0.1-3              
 [41] dichromat_2.0-0               htmltools_0.3.5              
 [43] ensembldb_1.6.2               BSgenome_1.42.0              
 [45] htmlwidgets_0.8               PFAM.db_3.4.0                
 [47] RSQLite_1.1-2                 shiny_1.0.0                  
 [49] GOstats_2.40.0                hwriter_1.3.2                
 [51] gtools_3.5.0                  BiocParallel_1.8.1           
 [53] R.oo_1.21.0                   acepack_1.4.1                
 [55] VariantAnnotation_1.20.2      RCurl_1.95-4.8               
 [57] magrittr_1.5                  GO.db_3.4.0                  
 [59] Formula_1.2-1                 oligoClasses_1.36.0          
 [61] Matrix_1.2-7.1                Rcpp_0.12.9                  
 [63] munsell_0.4.3                 S4Vectors_0.12.1             
 [65] R.methodsS3_1.7.1             stringi_1.1.2                
 [67] yaml_2.1.14                   edgeR_3.16.5                 
 [69] SummarizedExperiment_1.4.0    zlibbioc_1.20.0              
 [71] gplots_3.0.1                  plyr_1.8.4                   
 [73] AnnotationHub_2.6.4           grid_3.3.2                   
 [75] gdata_2.17.0                  ReportingTools_2.14.0        
 [77] lattice_0.20-34               Biostrings_2.42.1            
 [79] splines_3.3.2                 GenomicFeatures_1.26.2       
 [81] annotate_1.52.1               locfit_1.5-9.1               
 [83] knitr_1.15.1                  GenomicRanges_1.26.2         
 [85] codetools_0.2-15              geneplotter_1.52.0           
 [87] reshape2_1.4.2                biomaRt_2.30.0               
 [89] stats4_3.3.2                  XML_3.98-1.5                 
 [91] biovizBase_1.22.0             latticeExtra_0.6-28          
 [93] data.table_1.10.0             foreach_1.4.3                
 [95] httpuv_1.3.3                  gtable_0.2.0                 
 [97] reshape_0.8.6                 assertthat_0.1               
 [99] ggplot2_2.2.1                 mime_0.5                     
[101] xtable_1.8-2                  ff_2.2-13                    
[103] survival_2.40-1               tibble_1.2                   
[105] OrganismDbi_1.16.0            iterators_1.0.8              
[107] GenomicAlignments_1.10.0      AnnotationDbi_1.36.1         
[109] memoise_1.0.0                 IRanges_2.8.1                
[111] cluster_2.0.5                 interactiveDisplayBase_1.12.0
[113] GSEABase_1.36.0              
> 

 

ADD COMMENTlink written 20 months ago by Jenny Drnevich1.9k
0
gravatar for James W. MacDonald
20 months ago by
United States
James W. MacDonald47k wrote:

The error from affycoretools has to do with a conversion I made in plotPCA to using S4 methods, in which I forgot to include a method for matrix objects. That's fixed now, but doesn't yet appear to have propagated through the build servers yet.

As for the warnings, this was introduced by Herve recently, and backed out in devel, but not yet on release:

------------------------------------------------------------------------
r125890 | hpages@fhcrc.org | 2017-01-11 18:21:51 -0800 (Wed, 11 Jan 2017) | 11 lines
Changed paths:
   M /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/DESCRIPTION
   M /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/R/AnnDbPkg-templates-common.R
   M /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/R/loadDb.R
   A /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/R/utils.R (from /trunk/madman/Rpacks/AnnotationDbi/R/utils.R:125889)

Use 'vsf="unix-none"' when calling dbConnect() to connect to the db contained
in our SQLite-based annotation data packages (e.g. OrgDb, ChipDb, TxDb etc...
packages). This is to avoid the infamous "database is locked" error that some
users have reported on a few occasions in the past 10 years (and that we were
never able to reproduce). This was reported again recently by Rob Bradley at
Fred Hutch. Rob was trying to access TxDb.Hsapiens.UCSC.hg19.knownGene from
multiple nodes on the Hutch cluster where TxDb.Hsapiens.UCSC.hg19.knownGene is
installed on an NFS file system. Many thanks to Ben McGough, System Administra-
tor at the Hutch, for investigating this and suggesting the 'vsf="unix-none"'
solution!

------------------------------------------------------------------------

In devel we have an additional commit:

------------------------------------------------------------------------
r126087 | hpages@fhcrc.org | 2017-01-22 23:16:08 -0800 (Sun, 22 Jan 2017) | 1 line
Changed paths:
   M /trunk/madman/Rpacks/AnnotationDbi/R/utils.R

don't use 'vsf="unix-none"' on Windows
------------------------------------------------------------------------


I think these are just irritating warnings, rather than something you need to worry about.

 

ADD COMMENTlink written 20 months ago by James W. MacDonald47k
Ha! So the problem was with affycoretools :P I’ll be patient and wait for the next upgrade to become available. Thanks, Jim! From: James W. MacDonald [bioc] [mailto:noreply@bioconductor.org] Sent: Friday, January 27, 2017 10:17 AM To: Zadeh, Jenny Drnevich <drnevich@illinois.edu> Subject: [bioc] A: Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="&lt;a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=DwMDaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6-Bh1FprrmfLCzuKMeeZ1IaQQqjRPj_xNcuCh6hXgSU&m=tHiMdEbYVHoeR300g2HvVt30RipF2gIwz00D3ynsM_8&s=Nzpax-_cJTdKWm53bw42PukItiIc9Dr79PrY3DL6sBM&e="> User James W. MacDonald<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_5106_&amp;d=DwMDaQ&amp;c=8hUWFZcy2Z-Za5rBPlktOQ&amp;r=6-Bh1FprrmfLCzuKMeeZ1IaQQqjRPj_xNcuCh6hXgSU&amp;m=tHiMdEbYVHoeR300g2HvVt30RipF2gIwz00D3ynsM_8&amp;s=xyJjjN3tXkNIttgabxo6W8Ll6j6jRl4AeZ4tThGECao&amp;e="> wrote Answer: Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_91681_-2391683&amp;d=DwMDaQ&amp;c=8hUWFZcy2Z-Za5rBPlktOQ&amp;r=6-Bh1FprrmfLCzuKMeeZ1IaQQqjRPj_xNcuCh6hXgSU&amp;m=tHiMdEbYVHoeR300g2HvVt30RipF2gIwz00D3ynsM_8&amp;s=tLDAfkts9P917Q930Wc8vOdeJPOpC7jbsepjClgiT6E&amp;e=">: The error from affycoretools has to do with a conversion I made in plotPCA to using S4 methods, in which I forgot to include a method for matrix objects. That's fixed now, but doesn't yet appear to have propagated through the build servers yet. As for the warnings, this was introduced by Herve recently, and backed out in devel, but not yet on release: ------------------------------------------------------------------------ r125890 | hpages@fhcrc.org<mailto:hpages@fhcrc.org> | 2017-01-11 18:21:51 -0800 (Wed, 11 Jan 2017) | 11 lines Changed paths: M /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/DESCRIPTION M /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/R/AnnDbPkg-templates-common.R M /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/R/loadDb.R A /branches/RELEASE_3_4/madman/Rpacks/AnnotationDbi/R/utils.R (from /trunk/madman/Rpacks/AnnotationDbi/R/utils.R:125889) Use 'vsf="unix-none"' when calling dbConnect() to connect to the db contained in our SQLite-based annotation data packages (e.g. OrgDb, ChipDb, TxDb etc... packages). This is to avoid the infamous "database is locked" error that some users have reported on a few occasions in the past 10 years (and that we were never able to reproduce). This was reported again recently by Rob Bradley at Fred Hutch. Rob was trying to access TxDb.Hsapiens.UCSC.hg19.knownGene from multiple nodes on the Hutch cluster where TxDb.Hsapiens.UCSC.hg19.knownGene is installed on an NFS file system. Many thanks to Ben McGough, System Administra- tor at the Hutch, for investigating this and suggesting the 'vsf="unix-none"' solution! ------------------------------------------------------------------------ In devel we have an additional commit: ------------------------------------------------------------------------ r126087 | hpages@fhcrc.org<mailto:hpages@fhcrc.org> | 2017-01-22 23:16:08 -0800 (Sun, 22 Jan 2017) | 1 line Changed paths: M /trunk/madman/Rpacks/AnnotationDbi/R/utils.R don't use 'vsf="unix-none"' on Windows ------------------------------------------------------------------------ I think these are just irritating warnings, rather than something you need to worry about. ________________________________ Post tags: affycoretools You may reply via email or visit A: Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization
ADD REPLYlink written 20 months ago by Jenny Drnevich1.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 139 users visited in the last hour