Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
On 04/20/2017 03:08 AM, Michael Stadler wrote: Dear Martin, I've now spend a day trying to resolve this. To make a long story short: I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile and work under macOS Sierra. I tried updating bowtie, but: - bowtie 1.2 has a bug that prevents it from using multiple threads, which I could reproduce both under Linux and macOS Sierra and which I could not resolve (see https://github.com/BenLangmead/bowtie/issues/41). - bowtie 1.1.2 crashes if compiled with clang (see https://github.com/BenLangmead/bowtie/issues/21), the only known workaround being to use a different toolchain, which I think is not an option for BioC/Rbowtie. I hope that resolves also the issue on El Capitan. Thanks, it seems like the best available solution. Martin Michael On 19.04.2017 13:47, Martin Morgan wrote: On 04/19/2017 05:45 AM, Michael Stadler wrote: Dear BioC core, Thanks for the report, Herve. If I understand correctly, there is nothing I can do at this point to make QuasR green on windows, correct? I have another question regarding QuasR not building on veracruz2: The vignette does not build currently, reporting: Error on veracruz2.bioconductor.org processing sample /tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal: samtools invoked 'abort' ... Though it seems to build fine on other platforms, and there were no recent changes to the vignette. What would you or other suggest to do about that? The error is in createGenomicAlignmentsController after https://github.com/Bioconductor-mirror/QuasR/blob/cc374678033055f2bd4d105c502a426807223c1c/R/createAlignments-functions.R#L292 it looks like the sam file is quite funky Browse[4]> options(nwarnings=1) Browse[4]> xx = readLines(samFile) There were 2339 warnings (use warnings() to see them) Browse[4]> head(warnings(), 3) Warning messages: 1: In readLines(samFile) : line 7 appears to contain an embedded nul 2: In readLines(samFile) : line 8 appears to contain an embedded nul 3: In readLines(samFile) : line 9 appears to contain an embedded nul Browse[4]> table(nzchar(xx)) FALSE TRUE 2341 261 Browse[4]> substring(head(xx, 10), 1, 70) [1] "@HD\tVN:1.0\tSO:unsorted" [2] "@SQ\tSN:chr1\tLN:4" [3] "@SQ\tSN:chr2\tLN:1" [4] "@SQ\tSN:chr3\tLN:45000" [5] "@PG\tID:Bowtie\tVN:1.1.1\tCL:\"/Library/Frameworks/R.framework/Versions/3." [6] "" [7] "" [8] "" [9] "" [10] "" The 'abort' from Rsamtools is Parse error at line 143: missing colon in auxiliary data It's not really clear whether R is being confused by the embedded nulls or blank lines or other problem Browse[4]> xx[140 + 1:5] [1] "" "" "" "" "" Browse[4]> xx[nzhchar(xx)][140 + 1:5] Error in nzhchar(xx) : could not find function "nzhchar" Browse[4]> xx[nzchar(xx)][140 + 1:5] [1] "seq10137\t4\t*\t0\t0\t*\t*\t0\t0\tTCGTTATGGTTTCCGTTGCTGCCATCTCACAT\tB@BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0" [2] "seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBB@CBBBA9BB@>'>9@AA=A?\tXM:i:0" [3] "seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBC=A@BAABBABBA=A??><\tXM:i:0" [4] "seq10140\t4\t*\t0\t0\t*\t*\t0\t0\tGGTTGTCAGCGTCATAAGAGGACCTCCAAATG\t;;;AA=AA<AA<ABBB?=@>>=CCBB>9@@>B=BB=\tXM:i:0" [5] "seq10141\t4\t*\t0\t0\t*\t*\t0\t0\tAACCCTAATGAGCTTAATCAAGATGATGCTCGTTAT\tBBAB@AAB@BBBA@B@ABAABBABAA@B?A?@\tXM:i:0" So I guess it's in creation of the sam file -- Bowtie? Martin Any suggestions are appreciated, Michael On 17.04.2017 02:08, Hervé Pagès wrote: 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.mor...@roswellpark.org] Sent: Tuesday, 11 April 2017 7:20 PM To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@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
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Dear Martin, I've now spend a day trying to resolve this. To make a long story short: I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile and work under macOS Sierra. I tried updating bowtie, but: - bowtie 1.2 has a bug that prevents it from using multiple threads, which I could reproduce both under Linux and macOS Sierra and which I could not resolve (see https://github.com/BenLangmead/bowtie/issues/41). - bowtie 1.1.2 crashes if compiled with clang (see https://github.com/BenLangmead/bowtie/issues/21), the only known workaround being to use a different toolchain, which I think is not an option for BioC/Rbowtie. I hope that resolves also the issue on El Capitan. Michael On 19.04.2017 13:47, Martin Morgan wrote: > On 04/19/2017 05:45 AM, Michael Stadler wrote: >> Dear BioC core, >> >> Thanks for the report, Herve. If I understand correctly, there is >> nothing I can do at this point to make QuasR green on windows, correct? >> >> I have another question regarding QuasR not building on veracruz2: The >> vignette does not build currently, reporting: >> Error on veracruz2.bioconductor.org processing sample >> /tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal: >> samtools invoked 'abort' ... >> >> Though it seems to build fine on other platforms, and there were no >> recent changes to the vignette. What would you or other suggest to do >> about that? > > The error is in createGenomicAlignmentsController after > > https://github.com/Bioconductor-mirror/QuasR/blob/cc374678033055f2bd4d105c502a426807223c1c/R/createAlignments-functions.R#L292 > > > it looks like the sam file is quite funky > > Browse[4]> options(nwarnings=1) > Browse[4]> xx = readLines(samFile) > There were 2339 warnings (use warnings() to see them) > Browse[4]> head(warnings(), 3) > Warning messages: > 1: In readLines(samFile) : line 7 appears to contain an embedded nul > 2: In readLines(samFile) : line 8 appears to contain an embedded nul > 3: In readLines(samFile) : line 9 appears to contain an embedded nul > Browse[4]> table(nzchar(xx)) > > FALSE TRUE > 2341 261 > Browse[4]> substring(head(xx, 10), 1, 70) > [1] "@HD\tVN:1.0\tSO:unsorted" > [2] "@SQ\tSN:chr1\tLN:4" > [3] "@SQ\tSN:chr2\tLN:1" > [4] "@SQ\tSN:chr3\tLN:45000" > [5] > "@PG\tID:Bowtie\tVN:1.1.1\tCL:\"/Library/Frameworks/R.framework/Versions/3." > > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > > The 'abort' from Rsamtools is > > Parse error at line 143: missing colon in auxiliary data > > It's not really clear whether R is being confused by the embedded nulls > or blank lines or other problem > > Browse[4]> xx[140 + 1:5] > [1] "" "" "" "" "" > Browse[4]> xx[nzhchar(xx)][140 + 1:5] > Error in nzhchar(xx) : could not find function "nzhchar" > Browse[4]> xx[nzchar(xx)][140 + 1:5] > [1] > "seq10137\t4\t*\t0\t0\t*\t*\t0\t0\tTCGTTATGGTTTCCGTTGCTGCCATCTCACAT\tB@BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0" > > [2] > "seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBB@CBBBA9BB@>'>9@AA=A?\tXM:i:0" > > [3] > "seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBC=A@BAABBABBA=A??><\tXM:i:0" > > [4] > "seq10140\t4\t*\t0\t0\t*\t*\t0\t0\tGGTTGTCAGCGTCATAAGAGGACCTCCAAATG\t;;;AA=AA<AA<ABBB?=@>>=CCBB>9@@>B=BB=\tXM:i:0" > > [5] > "seq10141\t4\t*\t0\t0\t*\t*\t0\t0\tAACCCTAATGAGCTTAATCAAGATGATGCTCGTTAT\tBBAB@AAB@BBBA@B@ABAABBABAA@B?A?@\tXM:i:0" > > > So I guess it's in creation of the sam file -- Bowtie? > > Martin > >> >> Any suggestions are appreciated, >> Michael >> >> >> >> On 17.04.2017 02:08, Hervé Pagès wrote: >>> 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 M
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
On 04/19/2017 02:45 AM, Michael Stadler wrote:
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
Nothing you can do in QuasR itself. Sorry that I don't have time to do
this but someone would need to take a close look at this problem though.
And report his/her findings to the R folks. We're running short of time!
(will be a bummer to have R 3.4 released with such a nasty bug in it)
Cheers,
H.
I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on veracruz2.bioconductor.org processing sample
/tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal:
samtools invoked 'abort' ...
Though it seems to build fine on other platforms, and there were no
recent changes to the vignette. What would you or other suggest to do
about that?
Any suggestions are appreciated,
Michael
On 17.04.2017 02:08, Hervé Pagès wrote:
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.mor...@roswellpark.org]
Sent: Tuesday, 11 April 2017 7:20 PM
To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@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@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()
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Hi Michael, On 04/17/2017 12:31 PM, Michael Love wrote: alpine, which had this error as of Sunday, is now cleared (I didn't make any changes to the code) https://urldefense.proofpoint.com/v2/url?u=http-3A__master.bioconductor.org_checkResults_devel_bioc-2DLATEST_alpine_=DwIBaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=FslFDEAm_2UTMu0mMv7oNRUhFjxa9R6r2QKfY7_-ZZ8=NeikP8-8_2PSFQMJ7jiSmXUW4SWzjK-XZXnXqRAf3_U= The problem seems intermittent. All the packages that make direct or indirect calls to installed.packages() are not necessarily affected every day. Today the victims are: cobindR debrowser fCI GenomicFeatures GGBase QuasR So more victims than 3 days ago. Tomorrow we might see something different. H. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Dear Martin,
Thank you for the quick response - you are right to suspect bowtie, it
seems that version 1.1.1 which I am using in Rbowtie has an issue on
newer macOS versions, and I am currently looking into wether an update
to version 1.2 would fix this.
A first issue that I stumbled into is that R CMD check now warns about
the bowtie code using C++11 extensions. Following the manual, I have
added the following to DESCRIPTION:
SystemRequirements: GNU make, C++11
("GNU make" was already there), but the field seems to be ignored by R
CMD check and the warning persists. Is this something to worry about?
I hope to get back with a solution for the bowtie issue soon.
Michael
On 19.04.2017 13:47, Martin Morgan wrote:
> On 04/19/2017 05:45 AM, Michael Stadler wrote:
>> Dear BioC core,
>>
>> Thanks for the report, Herve. If I understand correctly, there is
>> nothing I can do at this point to make QuasR green on windows, correct?
>>
>> I have another question regarding QuasR not building on veracruz2: The
>> vignette does not build currently, reporting:
>> Error on veracruz2.bioconductor.org processing sample
>> /tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal:
>> samtools invoked 'abort' ...
>>
>> Though it seems to build fine on other platforms, and there were no
>> recent changes to the vignette. What would you or other suggest to do
>> about that?
>
> The error is in createGenomicAlignmentsController after
>
> https://github.com/Bioconductor-mirror/QuasR/blob/cc374678033055f2bd4d105c502a426807223c1c/R/createAlignments-functions.R#L292
>
>
> it looks like the sam file is quite funky
>
> Browse[4]> options(nwarnings=1)
> Browse[4]> xx = readLines(samFile)
> There were 2339 warnings (use warnings() to see them)
> Browse[4]> head(warnings(), 3)
> Warning messages:
> 1: In readLines(samFile) : line 7 appears to contain an embedded nul
> 2: In readLines(samFile) : line 8 appears to contain an embedded nul
> 3: In readLines(samFile) : line 9 appears to contain an embedded nul
> Browse[4]> table(nzchar(xx))
>
> FALSE TRUE
> 2341 261
> Browse[4]> substring(head(xx, 10), 1, 70)
> [1] "@HD\tVN:1.0\tSO:unsorted"
> [2] "@SQ\tSN:chr1\tLN:4"
> [3] "@SQ\tSN:chr2\tLN:1"
> [4] "@SQ\tSN:chr3\tLN:45000"
> [5]
> "@PG\tID:Bowtie\tVN:1.1.1\tCL:\"/Library/Frameworks/R.framework/Versions/3."
>
> [6] ""
> [7] ""
> [8] ""
> [9] ""
> [10] ""
>
> The 'abort' from Rsamtools is
>
> Parse error at line 143: missing colon in auxiliary data
>
> It's not really clear whether R is being confused by the embedded nulls
> or blank lines or other problem
>
> Browse[4]> xx[140 + 1:5]
> [1] "" "" "" "" ""
> Browse[4]> xx[nzhchar(xx)][140 + 1:5]
> Error in nzhchar(xx) : could not find function "nzhchar"
> Browse[4]> xx[nzchar(xx)][140 + 1:5]
> [1]
> "seq10137\t4\t*\t0\t0\t*\t*\t0\t0\tTCGTTATGGTTTCCGTTGCTGCCATCTCACAT\tB@BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0"
>
> [2]
> "seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBB@CBBBA9BB@>'>9@AA=A?\tXM:i:0"
>
> [3]
> "seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBC=A@BAABBABBA=A??><\tXM:i:0"
>
> [4]
> "seq10140\t4\t*\t0\t0\t*\t*\t0\t0\tGGTTGTCAGCGTCATAAGAGGACCTCCAAATG\t;;;AA=AA<AA<ABBB?=@>>=CCBB>9@@>B=BB=\tXM:i:0"
>
> [5]
> "seq10141\t4\t*\t0\t0\t*\t*\t0\t0\tAACCCTAATGAGCTTAATCAAGATGATGCTCGTTAT\tBBAB@AAB@BBBA@B@ABAABBABAA@B?A?@\tXM:i:0"
>
>
> So I guess it's in creation of the sam file -- Bowtie?
>
> Martin
>
>>
>> Any suggestions are appreciated,
>> Michael
>>
>>
>>
>> On 17.04.2017 02:08, Hervé Pagès wrote:
>>> 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-
>>
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on veracruz2.bioconductor.org processing sample
/tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal:
samtools invoked 'abort' ...
Though it seems to build fine on other platforms, and there were no
recent changes to the vignette. What would you or other suggest to do
about that?
Any suggestions are appreciated,
Michael
On 17.04.2017 02:08, Hervé Pagès wrote:
> 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.mor...@roswellpark.org]
>>> Sent: Tuesday, 11 April 2017 7:20 PM
>>> To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@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]))
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
alpine, which had this error as of Sunday, is now cleared (I didn't make any changes to the code) http://master.bioconductor.org/checkResults/devel/bioc-LATEST/alpine/ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
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.mor...@roswellpark.org]
Sent: Tuesday, 11 April 2017 7:20 PM
To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@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@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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qQj20RkrlTIRAItC
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,License,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@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://bioconductor.org/biocLite.R;)
trying URL
'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInst
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,
http://www.statsci.org/smyth
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
___
Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
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
> -Original Message-
> From: Gordon K Smyth
> Sent: Tuesday, 11 April 2017 6:26 PM
> To: bioc-devel@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://bioconductor.org/biocLite.R;)
> trying URL
> 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInst
> 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,
> http://www.statsci.org/smyth
___
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] 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://bioconductor.org/biocLite.R;)
trying URL
'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInstaller_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,
http://www.statsci.org/smyth
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
