[Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Hervé Pagès
hpages at fredhutch.org
Mon Apr 17 02:08:59 CEST 2017
FWIW here are all the packages that are victim of this
installed.packages bug in today's build report:
alpine
fCI
GenomicFeatures
QuasR
We only see this error on tokay2 (Windows).
H.
On 04/11/2017 04:21 PM, Gordon K Smyth wrote:
> I restarted my PC this morning and the problem disappeared.
>
> I probably should have tried that last night, but it was late ...
>
> Thanks
> Gordon
>
>> -----Original Message-----
>> From: Martin Morgan [mailto:martin.morgan at roswellpark.org]
>> Sent: Tuesday, 11 April 2017 7:20 PM
>> To: Gordon K Smyth <smyth at wehi.edu.au>; bioc-devel at r-project.org
>> Subject: Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
>>
>> On 04/11/2017 05:01 AM, Gordon K Smyth wrote:
>>> The problem appears to be with installed.packages(). If I start a fresh R
>> 3.4.0beta session, then I can run installed.packages() once with correct results,
>> but running it a second time gives the error message:
>>>
>>>> installed.packages()
>>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && :
>>> missing value where TRUE/FALSE needed
>>
>> The test is in this code chunk, from utils/R/packages.R
>>
>> for(lib in lib.loc) {
>> if(noCache) {
>> ret0 <- .readPkgDesc(lib, fields)
>> if(length(ret0)) retval <- rbind(retval, ret0)
>> } else {
>> ## Previously used URLencode for e.g. Windows paths with drives
>> ## This version works for very long file names.
>> base <- paste(c(lib, fields), collapse = ",")
>> ## add length and 64-bit CRC in hex (in theory, seems
>> ## it is actually 32-bit on some systems)
>> enc <- sprintf("%d_%s", nchar(base), .Call(C_crc64, base))
>> dest <- file.path(tempdir(), paste0("libloc_", enc, ".rds"))
>> if(file.exists(dest) &&
>> file.mtime(dest) > file.mtime(lib) &&
>> (val <- readRDS(dest))$base == base)
>> ## use the cache file
>> retval <- rbind(retval, val$value)
>> else {
>> ret0 <- .readPkgDesc(lib, fields)
>> if(length(ret0)) {
>> retval <- rbind(retval, ret0)
>> ## save the cache file
>> saveRDS(list(base = base, value = ret0), dest)
>> }
>> }
>> }
>>
>>
>> where 'lib' is one of .libPaths(), 'dest' is one of
>>
>> dir(tempdir(), pattern="libloc_", full=TRUE)
>>
>> and 'base' should be a character(1)
>>
>> I think the code chunk has tried to cache the packages installed in each
>> directory of .libPaths() (the saveRDS() line), and these are somehow
>> corrupted on the second time through (I guess evaluating the readRDS()??).
>>
>> For instance I have two paths in .libPaths() and after the first
>> install.packages() I have
>>
>> > str(readRDS(dir(tempdir(), full=TRUE)[1]))
>> List of 2
>> $ base : chr
>> "/home/mtmorgan/bin/R-3-4-
>> branch/library,Version,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,Li
>> cense,Li"|
>> __truncated__
>> $ value: chr [1:29, 1:17] "base" "boot" "class" "cluster" ...
>> > str(readRDS(dir(tempdir(), full=TRUE)[2]))
>> List of 2
>> $ base : chr
>> "/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-
>> 3.5,Version,Priority,Depends,Imports,LinkingTo,Suggests,E"|
>> __truncated__
>> $ value: chr [1:513, 1:17] "abind" "acepack" "aCGH" "ADaCGH2" ...
>>
>> I'm guessing that one of these files is corrupted somehow, but it's not
>> obvious how. Can you use options(error=recover) and find the values that
>> cause the conditional to fail?
>>
>> Martin
>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: Gordon K Smyth
>>>> Sent: Tuesday, 11 April 2017 6:26 PM
>>>> To: bioc-devel at r-project.org
>>>> Subject: Using BiocInstaller with R 3.4.0 beta
>>>>
>>>> I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the
>>>> BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an
>> error
>>>> message as shown below.
>>>>
>>>> What have I overlooked?
>>>>
>>>> Thanks
>>>> Gordon
>>>>
>>>>> sessionInfo()
>>>> R version 3.4.0 beta (2017-04-08 r72499)
>>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>>>
>>>> Matrix products: default
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
>>>> LC_MONETARY=English_Australia.1252
>>>> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_3.4.0
>>>>> remove.packages("BiocInstaller")
>>>> Removing package from 'C:/lib/R/R-3.4.0beta/library'
>>>> (as 'lib' is unspecified)
>>>> Error in find.package(pkgs, lib) :
>>>> there is no package called 'BiocInstaller'
>>>>> source("https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_biocLite.R&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=6ODigHgwIN79ejt5MJf2kpj1UREzVRkiKBpOWsY_J-I&e= ")
>>>> trying URL
>>>>
>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.5_bioc_bin_windows_contrib_3.4_BiocInst&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=n0cklbnoQ9a2xy8zQvs0mMdS3tP5gk2NbVWsALYoXOk&e=
>>>> aller_1.25.3.zip'
>>>> Content type 'application/zip' length 127489 bytes (124 KB)
>>>> downloaded 124 KB
>>>>
>>>> package 'BiocInstaller' successfully unpacked and MD5 sums checked
>>>>
>>>> The downloaded binary packages are in
>>>>
>>>> C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
>>>> Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
>>>>> BiocInstaller::biocValid()
>>>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && :
>>>> missing value where TRUE/FALSE needed
>>>>
>>>>
>>>> ---------------------------------------------
>>>> Professor Gordon K Smyth,
>>>> Head, Bioinformatics Division,
>>>> Walter and Eliza Hall Institute of Medical Research,
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.statsci.org_smyth&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=N8BZ6_dazp5kboftdMZCE4ip8G9ORI9zTd8TVRI4eB0&e=
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
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>>>
>>
>>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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