Re: [Bioc-devel] BioC 3.1 branch created
On Apr 16, 2015 9:44 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@r-project.org Sent: Thursday, April 16, 2015 6:57:45 PM Subject: Re: [Bioc-devel] BioC 3.1 branch created On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: The BioC 3.1 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be tomorrow if everything goes well) is in the 3.1 branch and accessible at: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ PKGNAME Only bug fixes and documentation improvements should go here. As always the devel version of your package is at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PKGNAME Similarly for experiment packages, where your package is available in devel at https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/PKGNAME The release branch of it is in: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/ PKGNAME Normal development of your package can now resume here. Please let us know if you have any questions. Was the wrong version bump done for the GitHub-SVN bridges, because the 'bioc-sync' commits show release version numbers and not devel ones?! Not the wrong version bump, but it seems like the second one didn't come through. Should be sorted now. Sorry for the inconvenience. Confirmed. And no worries. Thanks for your great work. Henrik Dan For instance, the aroma.light GitHub repository (master branch), which should reflect the Bioc devel version, 'bioc-sync' made a commit bumping the version from 1.39.5 to 1.40.0. Note that this version is the version for the Bioc release - not Bioc devel. I would expect it to be a bump to 1.41.0. Details: https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DESCRIPTION (1.41.0) I've verified that the bridge is still to the Bioc devel SVN (trunk/madman), because when I tweaked the Date in DESCRIPTION (with the wrong Version field) and pushed to GitHub, that was reflected on Bioc devel SVN (trunk/madman). I see the same for aroma.light as well: https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5da548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/DESCRIPTION (2.5.0) Holding back with pushes via GitHub until I resolved. Let me know if this is a FAQ. Thanks, Henrik Thanks! Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] AnnotationHubData Error: Access denied: 530
On 04/13/2015 02:48 AM, Thomas Maurel wrote:
Dear Martin,
I have investigated with our Web team and we believe that the command
attempts to open a number of concurrent sessions in order to download all of
the files. If that is the case then the problem is that our ftp server is
configured to limit the number of concurrent sessions per user in order to
prevent people using scripts to monopolise the server resources (and in some
cases accidentally DoS attack the server).
Hi Thomas -- thank you for trouble-shooting this.
The code used getURL(url, ...) without specifying a curl= argument. This causes
a new CURLHandle to be constructed for each call to getURL(). These are closed
when the garbage collector is run, but that is apparently too infrequent, and
expensive to run explicitly.
I updated the code to include the argument
curl=httr::handle_find(url)$handle
which re-uses httr's pool of url-specific handlers hence limiting the number of
simultaneous open connections. This seems to have been effective.
Thanks again,
Martin
Hope this helps, Regards, Thomas
On 10 Apr 2015, at 13:40, Thomas Maurel mau...@ebi.ac.uk wrote:
Hi Martin,
On 10 Apr 2015, at 13:23, Martin Morgan mtmor...@fredhutch.org wrote:
On 04/10/2015 04:34 AM, Rainer Johannes wrote:
hi Martin,
but if that's true, then I will never have a way to test whether the
recipe actually works, right?
I guess I don't really know what I'm talking about, and that insert=FALSE
is intended to not actually do the insertion so that the (immediate)
problem is not with AnnotationHubData.
From the traceback below it seems like the error occurs in calls like the
following
library(RCurl)
getURL(ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/,
dirlistonly=TRUE)
This seems to sometimes work and sometimes not
urls[1]
[1] ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/
getURL(urls[1], dirlistonly=TRUE)
[1] Ailuropoda_melanoleuca.ailMel1.78.gtf.gz\nCHECKSUMS\nREADME\n
getURL(urls[1], dirlistonly=TRUE)
[1] Ailuropoda_melanoleuca.ailMel1.78.gtf.gz\nCHECKSUMS\nREADME\n
getURL(urls[1], dirlistonly=TRUE)
Error in function (type, msg, asError = TRUE) : Access denied: 530
You are right, I�ve noticed the same thing. I will investigate and see if
there is something wrong with our FTP site machine.
Regards, Thomas
that's the full traceback:
updateResources(AnnotationHubRoot=getWd(),
BiocVersion=biocVersion(),
preparerClasses=EnsemblGtfToEnsDbPreparer, insert=FALSE,
metadataOnly=TRUE) INFO [2015-04-10 13:32:18] Preparer Class:
EnsemblGtfToEnsDbPreparer Ailuropoda_melanoleuca.ailMel1.78.gtf.gz
Anas_platyrhynchos.BGI_duck_1.0.78.gtf.gz
Anolis_carolinensis.AnoCar2.0.78.gtf.gz
Astyanax_mexicanus.AstMex102.78.gtf.gz Bos_taurus.UMD3.1.78.gtf.gz
Caenorhabditis_elegans.WBcel235.78.gtf.gz
Callithrix_jacchus.C_jacchus3.2.1.78.gtf.gz Error in function (type,
msg, asError = TRUE) : Access denied: 530
traceback()
17: fun(structure(list(message = msg, call = sys.call()), class =
c(typeName, GenericCurlError, error, condition))) 16: function
(type, msg, asError = TRUE) { if (!is.character(type)) { i =
match(type, CURLcodeValues) typeName = if (is.na(i)) character() else
names(CURLcodeValues)[i] } typeName = gsub(^CURLE_, , typeName) fun
= (if (asError) stop else warning) fun(structure(list(message = msg,
call = sys.call()), class = c(typeName, GenericCurlError, error,
condition))) }(67L, Access denied: 530, TRUE) 15:
.Call(R_curl_easy_perform, curl, .opts, isProtected, .encoding,
PACKAGE = RCurl) 14: curlPerform(curl = curl, .opts = opts, .encoding
= .encoding) 13: getURL(url, dirlistonly = TRUE) 12:
strsplit(getURL(url, dirlistonly = TRUE), \n) 11: (function (url,
filename, tag, verbose = TRUE) { df2 - strsplit(getURL(url,
dirlistonly = TRUE), \n)[[1]] df2 - df2[grep(paste0(filename, $),
df2)] drop - grepl(latest, df2) | grepl(00-, df2) df2 -
df2[!drop] df2 - paste0(url, df2) result - lapply(df2, function(x) {
if (verbose) message(basename(x)) tryCatch({ h =
suppressWarnings(GET(x, config = config(nobody = TRUE, filetime =
TRUE))) nams - names(headers(h)) if (last-modified %in% nams)
headers(h)[c(last-modified, content-length)] else c(`last-modified`
= NA, `content-length` = NA) }, error = function(err) {
warning(basename(x), : , conditionMessage(err)) list(`last-modified`
= character(), `content-length` = character()) }) }) size -
as.numeric(sapply(result, [[, content-length)) date -
strptime(sapply(result, [[, last-modified), %a, %d %b %Y
%H:%M:%S, tz = GMT) data.frame(fileurl = url, date, size, genome =
tag, stringsAsFactors = FALSE) })(dots[[1L]][[8L]], filename =
dots[[2L]][[1L]], tag = dots[[3L]][[8L]]) 10: mapply(FUN = f, ...,
SIMPLIFY = FALSE) 9: Map(.ftpFileInfo, urls, filename = gtf.gz, tag =
basename(urls)) 8: do.call(rbind, Map(.ftpFileInfo, urls, filename =
gtf.gz, tag
Re: [Bioc-devel] AnnotationHubData Error: Access denied: 530
Dear Martin,
On 17 Apr 2015, at 14:00, Martin Morgan mtmor...@fredhutch.org wrote:
On 04/13/2015 02:48 AM, Thomas Maurel wrote:
Dear Martin,
I have investigated with our Web team and we believe that the command
attempts to open a number of concurrent sessions in order to download all of
the files. If that is the case then the problem is that our ftp server is
configured to limit the number of concurrent sessions per user in order to
prevent people using scripts to monopolise the server resources (and in some
cases accidentally DoS attack the server).
Hi Thomas -- thank you for trouble-shooting this.
The code used getURL(url, ...) without specifying a curl= argument. This
causes a new CURLHandle to be constructed for each call to getURL(). These
are closed when the garbage collector is run, but that is apparently too
infrequent, and expensive to run explicitly.
I updated the code to include the argument
curl=httr::handle_find(url)$handle
which re-uses httr's pool of url-specific handlers hence limiting the number
of simultaneous open connections. This seems to have been effective.
Thanks again,
Martin
Thanks a lot for letting me know, I am happy to hear that you got to the bottom
of this issue.
Regards,
Thomas
Hope this helps, Regards, Thomas
On 10 Apr 2015, at 13:40, Thomas Maurel mau...@ebi.ac.uk wrote:
Hi Martin,
On 10 Apr 2015, at 13:23, Martin Morgan mtmor...@fredhutch.org wrote:
On 04/10/2015 04:34 AM, Rainer Johannes wrote:
hi Martin,
but if that's true, then I will never have a way to test whether the
recipe actually works, right?
I guess I don't really know what I'm talking about, and that insert=FALSE
is intended to not actually do the insertion so that the (immediate)
problem is not with AnnotationHubData.
From the traceback below it seems like the error occurs in calls like the
following
library(RCurl)
getURL(ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/,
dirlistonly=TRUE)
This seems to sometimes work and sometimes not
urls[1]
[1] ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/
getURL(urls[1], dirlistonly=TRUE)
[1] Ailuropoda_melanoleuca.ailMel1.78.gtf.gz\nCHECKSUMS\nREADME\n
getURL(urls[1], dirlistonly=TRUE)
[1] Ailuropoda_melanoleuca.ailMel1.78.gtf.gz\nCHECKSUMS\nREADME\n
getURL(urls[1], dirlistonly=TRUE)
Error in function (type, msg, asError = TRUE) : Access denied: 530
You are right, I�ve noticed the same thing. I will investigate and see if
there is something wrong with our FTP site machine.
Regards, Thomas
that's the full traceback:
updateResources(AnnotationHubRoot=getWd(),
BiocVersion=biocVersion(),
preparerClasses=EnsemblGtfToEnsDbPreparer, insert=FALSE,
metadataOnly=TRUE) INFO [2015-04-10 13:32:18] Preparer Class:
EnsemblGtfToEnsDbPreparer Ailuropoda_melanoleuca.ailMel1.78.gtf.gz
Anas_platyrhynchos.BGI_duck_1.0.78.gtf.gz
Anolis_carolinensis.AnoCar2.0.78.gtf.gz
Astyanax_mexicanus.AstMex102.78.gtf.gz Bos_taurus.UMD3.1.78.gtf.gz
Caenorhabditis_elegans.WBcel235.78.gtf.gz
Callithrix_jacchus.C_jacchus3.2.1.78.gtf.gz Error in function (type,
msg, asError = TRUE) : Access denied: 530
traceback()
17: fun(structure(list(message = msg, call = sys.call()), class =
c(typeName, GenericCurlError, error, condition))) 16: function
(type, msg, asError = TRUE) { if (!is.character(type)) { i =
match(type, CURLcodeValues) typeName = if (is.na(i)) character() else
names(CURLcodeValues)[i] } typeName = gsub(^CURLE_, , typeName) fun
= (if (asError) stop else warning) fun(structure(list(message = msg,
call = sys.call()), class = c(typeName, GenericCurlError, error,
condition))) }(67L, Access denied: 530, TRUE) 15:
.Call(R_curl_easy_perform, curl, .opts, isProtected, .encoding,
PACKAGE = RCurl) 14: curlPerform(curl = curl, .opts = opts, .encoding
= .encoding) 13: getURL(url, dirlistonly = TRUE) 12:
strsplit(getURL(url, dirlistonly = TRUE), \n) 11: (function (url,
filename, tag, verbose = TRUE) { df2 - strsplit(getURL(url,
dirlistonly = TRUE), \n)[[1]] df2 - df2[grep(paste0(filename, $),
df2)] drop - grepl(latest, df2) | grepl(00-, df2) df2 -
df2[!drop] df2 - paste0(url, df2) result - lapply(df2, function(x) {
if (verbose) message(basename(x)) tryCatch({ h =
suppressWarnings(GET(x, config = config(nobody = TRUE, filetime =
TRUE))) nams - names(headers(h)) if (last-modified %in% nams)
headers(h)[c(last-modified, content-length)] else c(`last-modified`
= NA, `content-length` = NA) }, error = function(err) {
warning(basename(x), : , conditionMessage(err)) list(`last-modified`
= character(), `content-length` = character()) }) }) size -
as.numeric(sapply(result, [[, content-length)) date -
strptime(sapply(result, [[, last-modified), %a, %d %b %Y
%H:%M:%S, tz = GMT) data.frame(fileurl = url, date, size,
Re: [Bioc-devel] BioC 3.1 branch created
Hi Kevin, Thanks, I will try it later and check whether I have still this issue to connect it. Tiphaine From: Kevin Rue-Albrecht kevin@ucdconnect.iemailto:kevin@ucdconnect.ie Date: Friday, 17 April 2015 11:30 To: Tiphaine Martin tiphaine.mar...@kcl.ac.ukmailto:tiphaine.mar...@kcl.ac.uk Cc: Dan Tenenbaum dtene...@fredhutch.orgmailto:dtene...@fredhutch.org, bioc-devel bioc-devel@r-project.orgmailto:bioc-devel@r-project.org Subject: Re: [Bioc-devel] BioC 3.1 branch created Hi Tiphaine, I have followed both of your links,. and they both work for me. Probably just a glitch in the connection ? Hi Dan, I have a quick question of my own, I would like to bridge the new release branch to my Github release repository, but: * In the dropdown of the bridge creation, release 3.0 is still listed. I supposed I should wait that 3.1 is listed there, to create the good bridge? * I had a GitHub repository bridged to the 3.0 release branch. Is it ok to use the same GitHub repository, and use SVN wins during the bridge creation? That should update GitHub with the new release code, right? Many thanks, Kevin On 17 April 2015 at 11:43, Martin, Tiphaine tiphaine.mar...@kcl.ac.ukmailto:tiphaine.mar...@kcl.ac.uk wrote: Hi Dan, When I try to access on my package, I have �Internal Server Error�. Maybe I make a mistake somewhere. https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ coMET https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET Regards, Tiphaine On 17/04/2015 05:44, Dan Tenenbaum dtene...@fredhutch.orgmailto:dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edumailto:henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.orgmailto:dtene...@fredhutch.org Cc: bioc-devel bioc-devel@r-project.orgmailto:bioc-devel@r-project.org Sent: Thursday, April 16, 2015 6:57:45 PM Subject: Re: [Bioc-devel] BioC 3.1 branch created On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum dtene...@fredhutch.orgmailto:dtene...@fredhutch.org wrote: The BioC 3.1 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be tomorrow if everything goes well) is in the 3.1 branch and accessible at: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/PKGNAME Only bug fixes and documentation improvements should go here. As always the devel version of your package is at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PKGNAME Similarly for experiment packages, where your package is available in devel at https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/PKGNAME The release branch of it is in: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs /PKGNAME Normal development of your package can now resume here. Please let us know if you have any questions. Was the wrong version bump done for the GitHub-SVN bridges, because the 'bioc-sync' commits show release version numbers and not devel ones?! Not the wrong version bump, but it seems like the second one didn't come through. Should be sorted now. Sorry for the inconvenience. Dan For instance, the aroma.light GitHub repository (master branch), which should reflect the Bioc devel version, 'bioc-sync' made a commit bumping the version from 1.39.5 to 1.40.0. Note that this version is the version for the Bioc release - not Bioc devel. I would expect it to be a bump to 1.41.0. Details: https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e 426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE SCRIPTION (1.41.0) I've verified that the bridge is still to the Bioc devel SVN (trunk/madman), because when I tweaked the Date in DESCRIPTION (with the wrong Version field) and pushed to GitHub, that was reflected on Bioc devel SVN (trunk/madman). I see the same for aroma.light as well: https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5d a548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/D ESCRIPTION (2.5.0) Holding back with pushes via GitHub until I resolved. Let me know if this is a FAQ. Thanks, Henrik Thanks! Dan ___ Bioc-devel@r-project.orgmailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.orgmailto:Bioc-devel@r-project.org
Re: [Bioc-devel] BioC 3.1 branch created
Hi Dan, When I try to access on my package, I have ³Internal Server Error². Maybe I make a mistake somewhere. https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ coMET https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET Regards, Tiphaine On 17/04/2015 05:44, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@r-project.org Sent: Thursday, April 16, 2015 6:57:45 PM Subject: Re: [Bioc-devel] BioC 3.1 branch created On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: The BioC 3.1 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be tomorrow if everything goes well) is in the 3.1 branch and accessible at: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/PKGNAME Only bug fixes and documentation improvements should go here. As always the devel version of your package is at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PKGNAME Similarly for experiment packages, where your package is available in devel at https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/PKGNAME The release branch of it is in: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs /PKGNAME Normal development of your package can now resume here. Please let us know if you have any questions. Was the wrong version bump done for the GitHub-SVN bridges, because the 'bioc-sync' commits show release version numbers and not devel ones?! Not the wrong version bump, but it seems like the second one didn't come through. Should be sorted now. Sorry for the inconvenience. Dan For instance, the aroma.light GitHub repository (master branch), which should reflect the Bioc devel version, 'bioc-sync' made a commit bumping the version from 1.39.5 to 1.40.0. Note that this version is the version for the Bioc release - not Bioc devel. I would expect it to be a bump to 1.41.0. Details: https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e 426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE SCRIPTION (1.41.0) I've verified that the bridge is still to the Bioc devel SVN (trunk/madman), because when I tweaked the Date in DESCRIPTION (with the wrong Version field) and pushed to GitHub, that was reflected on Bioc devel SVN (trunk/madman). I see the same for aroma.light as well: https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5d a548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/D ESCRIPTION (2.5.0) Holding back with pushes via GitHub until I resolved. Let me know if this is a FAQ. Thanks, Henrik Thanks! Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BioC 3.1 branch created
- Original Message - From: Kevin Rue-Albrecht kevin@ucdconnect.ie To: Tiphaine Martin tiphaine.mar...@kcl.ac.uk Cc: Dan Tenenbaum dtene...@fredhutch.org, bioc-devel bioc-devel@r-project.org Sent: Friday, April 17, 2015 4:30:24 AM Subject: Re: [Bioc-devel] BioC 3.1 branch created Hi Tiphaine, I have followed both of your links,. and they both work for me. Probably just a glitch in the connection ? Hi Dan, I have a quick question of my own, I would like to bridge the new release branch to my Github release repository, but: * In the dropdown of the bridge creation, release 3.0 is still listed. I supposed I should wait that 3.1 is listed there, to create the good bridge? I will probably remove the 3.0 bridges as we are not building that version anymore and commits to that branch are disabled. * I had a GitHub repository bridged to the 3.0 release branch. Is it ok to use the same GitHub repository, and use SVN wins during the bridge creation? That should update GitHub with the new release code, right? Yes. Delete your 3.0 bridge first. Dan Many thanks, Kevin On 17 April 2015 at 11:43, Martin, Tiphaine tiphaine.mar...@kcl.ac.uk wrote: Hi Dan, When I try to access on my package, I have ³Internal Server Error². Maybe I make a mistake somewhere. https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ coMET https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET Regards, Tiphaine On 17/04/2015 05:44, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@r-project.org Sent: Thursday, April 16, 2015 6:57:45 PM Subject: Re: [Bioc-devel] BioC 3.1 branch created On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: The BioC 3.1 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be tomorrow if everything goes well) is in the 3.1 branch and accessible at: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/PKGNAME Only bug fixes and documentation improvements should go here. As always the devel version of your package is at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ PKGNAME Similarly for experiment packages, where your package is available in devel at https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ PKGNAME The release branch of it is in: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs /PKGNAME Normal development of your package can now resume here. Please let us know if you have any questions. Was the wrong version bump done for the GitHub-SVN bridges, because the 'bioc-sync' commits show release version numbers and not devel ones?! Not the wrong version bump, but it seems like the second one didn't come through. Should be sorted now. Sorry for the inconvenience. Dan For instance, the aroma.light GitHub repository (master branch), which should reflect the Bioc devel version, 'bioc-sync' made a commit bumping the version from 1.39.5 to 1.40.0. Note that this version is the version for the Bioc release - not Bioc devel. I would expect it to be a bump to 1.41.0. Details: https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e 426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE SCRIPTION (1.41.0) I've verified that the bridge is still to the Bioc devel SVN (trunk/madman), because when I tweaked the Date in DESCRIPTION (with the wrong Version field) and pushed to GitHub, that was reflected on Bioc devel SVN (trunk/madman). I see the same for aroma.light as well: https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5d a548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack s/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/D ESCRIPTION (2.5.0) Holding back with pushes via GitHub until I resolved. Let me know if this is a FAQ. Thanks, Henrik Thanks! Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___
Re: [Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle
On 04/17/2015 10:00 AM, Michael Lawrence wrote:
Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.
Not sure what you mean. Can you give an example?
H.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Hi,
I think we should just expand the Rle internally. That will produce
a numeric vector of the length of the GRanges i.e. it will be the
same size as the start and end components of the GRanges object itself.
No big deal at all.
I'll make that change.
H.
On 04/17/2015 09:00 AM, Michael Lawrence wrote:
Ideally it should be supported, but it would take some work as
the coverage
stuff is all in C. Could you give more details on your use case? For
example, if you already have a range for every position on the
chromosome,
you could just extract the score column. I'm guessing it's more
complicated
than that. If the zeros are the problem, you could just subset
the GRanges
to remove the ranges with zero score, and then coerce the score
to numeric
before calling coverage.
Michael
2015-04-17 8:00 GMT-07:00 Philip Lijnzaad
p.lijnz...@umcutrecht.nl mailto:p.lijnz...@umcutrecht.nl:
Dear all, I'm puzzled by the following behaviour:
Given
n - 10
gr - GRanges(seqnames=Rle('A', n),
ranges=IRanges(1:n, width=1),
score=Rle(5,n))
If I do
coverage(gr,weight='score')
I get
Error in .normarg_shift_or_weight(weight, weight, x) :
'weight' must be a numeric vector, a single string,
or a list-like
object
Surely 'score' should be allowed to be an Rle? Especially
given the
fact that the return value of coverage(x,weight=score)
when score is
plain numeric vector is always an Rle ! Is this the expected
behaviour?
If so, I would argue that violates the principle of least
suprise :-)
The background to this is that I do numerical analysis on
derived
numerical data along my chromosomes. It contains many
contiguous zeroes so it would be wasteful to cast
everything down using as.numeric().
This is R version 3.01 on x86_64 Linux, Bioconductor version
2.13,
package.version(IRanges)
[1] 1.20.7
package.version(GenomicRanges)
[1] 1.14.4
Regards,
Philip
--
Philip Lijnzaad, PhD
Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 2.211
IM: plijnz...@jabber.org mailto:plijnz...@jabber.org ,
philip.lijnz...@gmail.com mailto:philip.lijnz...@gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464 tel:%2B31%20%280%298875%2068464
--
De informatie opgenomen in dit bericht kan vertrouwelijk
zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit
bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de
afzender
direct
te informeren door het bericht te retourneren. Het
Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in
de zin van de
W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat
geregistreerd
bij
de Kamer van Koophandel voor Midden-Nederland onder nr.
30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
--
This message may contain confidential information and
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___
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mailing list
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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: hpa...@fredhutch.org mailto:hpa...@fredhutch.org
Phone: (206) 667-5791 tel:%28206%29%20667-5791
Fax: (206) 667-1319
Re: [Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle
Hi,
I think we should just expand the Rle internally. That will produce
a numeric vector of the length of the GRanges i.e. it will be the
same size as the start and end components of the GRanges object itself.
No big deal at all.
I'll make that change.
H.
On 04/17/2015 09:00 AM, Michael Lawrence wrote:
Ideally it should be supported, but it would take some work as the coverage
stuff is all in C. Could you give more details on your use case? For
example, if you already have a range for every position on the chromosome,
you could just extract the score column. I'm guessing it's more complicated
than that. If the zeros are the problem, you could just subset the GRanges
to remove the ranges with zero score, and then coerce the score to numeric
before calling coverage.
Michael
2015-04-17 8:00 GMT-07:00 Philip Lijnzaad p.lijnz...@umcutrecht.nl:
Dear all, I'm puzzled by the following behaviour:
Given
n - 10
gr - GRanges(seqnames=Rle('A', n),
ranges=IRanges(1:n, width=1),
score=Rle(5,n))
If I do
coverage(gr,weight='score')
I get
Error in .normarg_shift_or_weight(weight, weight, x) :
'weight' must be a numeric vector, a single string, or a list-like
object
Surely 'score' should be allowed to be an Rle? Especially given the
fact that the return value of coverage(x,weight=score) when score is
plain numeric vector is always an Rle ! Is this the expected behaviour?
If so, I would argue that violates the principle of least suprise :-)
The background to this is that I do numerical analysis on derived
numerical data along my chromosomes. It contains many
contiguous zeroes so it would be wasteful to cast
everything down using as.numeric().
This is R version 3.01 on x86_64 Linux, Bioconductor version 2.13,
package.version(IRanges)
[1] 1.20.7
package.version(GenomicRanges)
[1] 1.14.4
Regards,
Philip
--
Philip Lijnzaad, PhD
Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 2.211
IM: plijnz...@jabber.org , philip.lijnz...@gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464
--
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender
direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd
bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
--
This message may contain confidential information and ...{{dropped:10}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle
Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès hpa...@fredhutch.org wrote:
Hi,
I think we should just expand the Rle internally. That will produce
a numeric vector of the length of the GRanges i.e. it will be the
same size as the start and end components of the GRanges object itself.
No big deal at all.
I'll make that change.
H.
On 04/17/2015 09:00 AM, Michael Lawrence wrote:
Ideally it should be supported, but it would take some work as the
coverage
stuff is all in C. Could you give more details on your use case? For
example, if you already have a range for every position on the chromosome,
you could just extract the score column. I'm guessing it's more
complicated
than that. If the zeros are the problem, you could just subset the GRanges
to remove the ranges with zero score, and then coerce the score to numeric
before calling coverage.
Michael
2015-04-17 8:00 GMT-07:00 Philip Lijnzaad p.lijnz...@umcutrecht.nl:
Dear all, I'm puzzled by the following behaviour:
Given
n - 10
gr - GRanges(seqnames=Rle('A', n),
ranges=IRanges(1:n, width=1),
score=Rle(5,n))
If I do
coverage(gr,weight='score')
I get
Error in .normarg_shift_or_weight(weight, weight, x) :
'weight' must be a numeric vector, a single string, or a list-like
object
Surely 'score' should be allowed to be an Rle? Especially given the
fact that the return value of coverage(x,weight=score) when score is
plain numeric vector is always an Rle ! Is this the expected behaviour?
If so, I would argue that violates the principle of least suprise :-)
The background to this is that I do numerical analysis on derived
numerical data along my chromosomes. It contains many
contiguous zeroes so it would be wasteful to cast
everything down using as.numeric().
This is R version 3.01 on x86_64 Linux, Bioconductor version 2.13,
package.version(IRanges)
[1] 1.20.7
package.version(GenomicRanges)
[1] 1.14.4
Regards,
Philip
--
Philip Lijnzaad, PhD
Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 2.211
IM: plijnz...@jabber.org , philip.lijnz...@gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464
--
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender
direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat
geregistreerd
bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
--
This message may contain confidential information and ...{{dropped:10}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
[[alternative HTML version deleted]]
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Re: [Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle
Ideally it should be supported, but it would take some work as the coverage
stuff is all in C. Could you give more details on your use case? For
example, if you already have a range for every position on the chromosome,
you could just extract the score column. I'm guessing it's more complicated
than that. If the zeros are the problem, you could just subset the GRanges
to remove the ranges with zero score, and then coerce the score to numeric
before calling coverage.
Michael
2015-04-17 8:00 GMT-07:00 Philip Lijnzaad p.lijnz...@umcutrecht.nl:
Dear all, I'm puzzled by the following behaviour:
Given
n - 10
gr - GRanges(seqnames=Rle('A', n),
ranges=IRanges(1:n, width=1),
score=Rle(5,n))
If I do
coverage(gr,weight='score')
I get
Error in .normarg_shift_or_weight(weight, weight, x) :
'weight' must be a numeric vector, a single string, or a list-like
object
Surely 'score' should be allowed to be an Rle? Especially given the
fact that the return value of coverage(x,weight=score) when score is
plain numeric vector is always an Rle ! Is this the expected behaviour?
If so, I would argue that violates the principle of least suprise :-)
The background to this is that I do numerical analysis on derived
numerical data along my chromosomes. It contains many
contiguous zeroes so it would be wasteful to cast
everything down using as.numeric().
This is R version 3.01 on x86_64 Linux, Bioconductor version 2.13,
package.version(IRanges)
[1] 1.20.7
package.version(GenomicRanges)
[1] 1.14.4
Regards,
Philip
--
Philip Lijnzaad, PhD
Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 2.211
IM: plijnz...@jabber.org , philip.lijnz...@gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464
--
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender
direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd
bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
--
This message may contain confidential information and ...{{dropped:10}}
___
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[Bioc-devel] R 3.3 for snow leopard
Hi, This is not BioC related, but should hopefully be quick. According to http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-R-under-OS-X there may be a separate installer package, R-3.3.0-snowleopard.pkg. I'm not seeing any at http://r.research.att.com/. Has anyone heard if they'll keep supporting snowleopard? If not, I guess it's finally time to upgrade to Mavericks or Yosemite: do you recommend any version in particular? If anyone has a list of tips for upgrading, it'd be great if you can share them. Thanks, Leo PS Some older threads of initial problems with Mavericks. I guess that there might be other problems with Yosemite. * https://hopstat.wordpress.com/2013/10/24/mavericks-and-rstudio/ * http://blog.rstudio.org/2013/11/12/rstudio-os-x-mavericks-issues-resolved/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R 3.3 for snow leopard
- Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: bioc-devel@r-project.org Sent: Friday, April 17, 2015 12:43:12 PM Subject: [Bioc-devel] R 3.3 for snow leopard Hi, This is not BioC related, but should hopefully be quick. According to http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-R-under-OS-X there may be a separate installer package, R-3.3.0-snowleopard.pkg. I'm not seeing any at http://r.research.att.com/. Has anyone heard if they'll keep supporting snowleopard? Don't draw any conclusions from this; I think it just isn't available yet. Note that R-3.2.0 is not yet available for either Mac platform. Dan If not, I guess it's finally time to upgrade to Mavericks or Yosemite: do you recommend any version in particular? If anyone has a list of tips for upgrading, it'd be great if you can share them. Thanks, Leo PS Some older threads of initial problems with Mavericks. I guess that there might be other problems with Yosemite. * https://hopstat.wordpress.com/2013/10/24/mavericks-and-rstudio/ * http://blog.rstudio.org/2013/11/12/rstudio-os-x-mavericks-issues-resolved/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3
- Original Message - From: Sergei Ryazansky s.ryazan...@gmail.com To: bioc-devel@r-project.org Sent: Friday, April 17, 2015 1:53:41 PM Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Hello everyone, after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and org.Hs.eg.db are failed to load (sorry for non-english environment): library(GO.db)Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ traceback()2: stop(gettextf(package or namespace load failed for %s, sQuote(package)), call. = FALSE, domain = NA) 1: library(GO.db) sessionInfo()R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] BiocInstaller_1.16.2 RSQLite_1.0.0DBI_0.3.1 AnnotationDbi_1.28.2 [5] GenomeInfoDb_1.2.5 IRanges_2.0.1S4Vectors_0.4.0 GEOquery_2.32.0 [9] Biobase_2.26.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2 colorspace_1.2-6 stringr_0.6.2 [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2 digest_0.6.8 [11] reshape2_1.4.1 ggplot2_1.0.1bitops_1.0-6 RCurl_1.95-4.5 scales_0.2.4 [16] XML_3.98-1.1 proto_0.3-10 Are there any way to fix this? After you upgrade to R-3.2.0 you need to upgrade all your packages with: library(BiocInstaller) biocLite() Dan -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3
Somewhere in GO.db a direct call to the ls .Internal is being made (probably a speed hack) apparently. The API for .Internal(ls()) has changed in R 3.2.0. This call should be replaced with names, which now works on environments in R 3.2.0, and is way faster than the direct call to .Internal(ls()) too. Regards, Pete Peter M. Haverty, Ph.D. Genentech, Inc. phave...@gene.com On Fri, Apr 17, 2015 at 1:53 PM, Sergei Ryazansky s.ryazan...@gmail.com wrote: Hello everyone, after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and org.Hs.eg.db are failed to load (sorry for non-english environment): library(GO.db)Error : .onLoad �� ��� � loadNamespace() ��� 'GO.db', ���: �: ls(envir, all.names = TRUE) ��: 2 � � .Internal(ls), � � 3��: �� ��� �� ��� ��� 'GO.db' traceback()2: stop(gettextf(package or namespace load failed for %s, sQuote(package)), call. = FALSE, domain = NA) 1: library(GO.db) sessionInfo()R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] BiocInstaller_1.16.2 RSQLite_1.0.0DBI_0.3.1 AnnotationDbi_1.28.2 [5] GenomeInfoDb_1.2.5 IRanges_2.0.1S4Vectors_0.4.0 GEOquery_2.32.0 [9] Biobase_2.26.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2 colorspace_1.2-6 stringr_0.6.2 [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2 digest_0.6.8 [11] reshape2_1.4.1 ggplot2_1.0.1bitops_1.0-6 RCurl_1.95-4.5 scales_0.2.4 [16] XML_3.98-1.1 proto_0.3-10 Are there any way to fix this? -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3
Thanks, it fixed the issue. 2015-04-18 0:24 GMT+03:00 Dan Tenenbaum dtene...@fredhutch.org: - Original Message - From: Sergei Ryazansky s.ryazan...@gmail.com To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Friday, April 17, 2015 2:18:00 PM Subject: Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Yes, I did the upgrading of Bioconductor as well, but the result was the same: library(BiocInstaller, lib.loc=~/Rlibs) Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.2.0. biocLite() should update itself to version 1.18.1 and then install from the proper place. We'll look into that, but try this: Start R with R --vanilla Then: remove.packages(BiocInstaller) source(http://bioconductor.org/biocLite.R;) biocLite() Dan Old packages: 'manipulate' Update all/some/none? [a/s/n]: n library(GO.db) Загрузка требуемого пакета: AnnotationDbi Загрузка требуемого пакета: stats4 Загрузка требуемого пакета: GenomeInfoDb Загрузка требуемого пакета: S4Vectors Загрузка требуемого пакета: IRanges Присоединяю пакет: ‘AnnotationDbi’ The following object is masked from ‘package:GenomeInfoDb’: species Загрузка требуемого пакета: DBI Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3 Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ 2015-04-18 0:11 GMT+03:00 Dan Tenenbaum dtene...@fredhutch.org : - Original Message - From: Sergei Ryazansky s.ryazan...@gmail.com To: bioc-devel@r-project.org Sent: Friday, April 17, 2015 1:53:41 PM Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Hello everyone, after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and org.Hs.eg.db are failed to load (sorry for non-english environment): library(GO.db)Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ traceback()2: stop(gettextf(package or namespace load failed for %s, sQuote(package)), call. = FALSE, domain = NA) 1: library(GO.db) sessionInfo()R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] BiocInstaller_1.16.2 RSQLite_1.0.0 DBI_0.3.1 AnnotationDbi_1.28.2 [5] GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0 GEOquery_2.32.0 [9] Biobase_2.26.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2 colorspace_1.2-6 stringr_0.6.2 [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2 digest_0.6.8 [11] reshape2_1.4.1 ggplot2_1.0.1 bitops_1.0-6 RCurl_1.95-4.5 scales_0.2.4 [16] XML_3.98-1.1 proto_0.3-10 Are there any way to fix this? After you upgrade to R-3.2.0 you need to upgrade all your packages with: library(BiocInstaller) biocLite() Dan -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Sincerely, Sergei Ryazansky, PhD IMG RAS, Moscow -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3
- Original Message - From: Sergei Ryazansky s.ryazan...@gmail.com To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Friday, April 17, 2015 2:18:00 PM Subject: Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Yes, I did the upgrading of Bioconductor as well, but the result was the same: library(BiocInstaller, lib.loc=~/Rlibs) Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.2.0. biocLite() should update itself to version 1.18.1 and then install from the proper place. We'll look into that, but try this: Start R with R --vanilla Then: remove.packages(BiocInstaller) source(http://bioconductor.org/biocLite.R;) biocLite() Dan Old packages: 'manipulate' Update all/some/none? [a/s/n]: n library(GO.db) Загрузка требуемого пакета: AnnotationDbi Загрузка требуемого пакета: stats4 Загрузка требуемого пакета: GenomeInfoDb Загрузка требуемого пакета: S4Vectors Загрузка требуемого пакета: IRanges Присоединяю пакет: ‘AnnotationDbi’ The following object is masked from ‘package:GenomeInfoDb’: species Загрузка требуемого пакета: DBI Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3 Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ 2015-04-18 0:11 GMT+03:00 Dan Tenenbaum dtene...@fredhutch.org : - Original Message - From: Sergei Ryazansky s.ryazan...@gmail.com To: bioc-devel@r-project.org Sent: Friday, April 17, 2015 1:53:41 PM Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Hello everyone, after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and org.Hs.eg.db are failed to load (sorry for non-english environment): library(GO.db)Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ traceback()2: stop(gettextf(package or namespace load failed for %s, sQuote(package)), call. = FALSE, domain = NA) 1: library(GO.db) sessionInfo()R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] BiocInstaller_1.16.2 RSQLite_1.0.0 DBI_0.3.1 AnnotationDbi_1.28.2 [5] GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0 GEOquery_2.32.0 [9] Biobase_2.26.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2 colorspace_1.2-6 stringr_0.6.2 [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2 digest_0.6.8 [11] reshape2_1.4.1 ggplot2_1.0.1 bitops_1.0-6 RCurl_1.95-4.5 scales_0.2.4 [16] XML_3.98-1.1 proto_0.3-10 Are there any way to fix this? After you upgrade to R-3.2.0 you need to upgrade all your packages with: library(BiocInstaller) biocLite() Dan -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Sincerely, Sergei Ryazansky, PhD IMG RAS, Moscow ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R 3.3 for snow leopard
Hej Leonardo, I had the same doubts when Maverick came out, but eventually went for it. Since then, I have been running R and RStudio on OSX Yosemite - since Yosemite got out - and never had any problems. There are been some issues originally with Maverick but these are history. You might need to install some of the additional libs detailed at http://r.research.att.com/ depending on the packages you want to use and you will need XCode to be installed but that's it really. What you need to be aware of, though, is if your Mac does not have an SDD drive but a classic harddrive you might experience a performance drop and at times very annoying lags after moving to Maverick or Yosemite. The performances of my older Mac (MacBook Pro from 2009 with an HDD) have significantly deteriorated since upgrading from Snow Leopard to Maverick to Yosemite. So much that I have/am considered/considering downgrading it. This is mere speculation, but I guess the newer OSX have not been developed and tested for classic harddrives, so I'm afraid that this situation is not going to improve. HTH, Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On 17 Apr 2015, at 21:47, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: bioc-devel@r-project.org Sent: Friday, April 17, 2015 12:43:12 PM Subject: [Bioc-devel] R 3.3 for snow leopard Hi, This is not BioC related, but should hopefully be quick. According to http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-R-under-OS-X there may be a separate installer package, R-3.3.0-snowleopard.pkg. I'm not seeing any at http://r.research.att.com/. Has anyone heard if they'll keep supporting snowleopard? Don't draw any conclusions from this; I think it just isn't available yet. Note that R-3.2.0 is not yet available for either Mac platform. Dan If not, I guess it's finally time to upgrade to Mavericks or Yosemite: do you recommend any version in particular? If anyone has a list of tips for upgrading, it'd be great if you can share them. Thanks, Leo PS Some older threads of initial problems with Mavericks. I guess that there might be other problems with Yosemite. * https://hopstat.wordpress.com/2013/10/24/mavericks-and-rstudio/ * http://blog.rstudio.org/2013/11/12/rstudio-os-x-mavericks-issues-resolved/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3
Hello everyone, after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and org.Hs.eg.db are failed to load (sorry for non-english environment): library(GO.db)Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ traceback()2: stop(gettextf(package or namespace load failed for %s, sQuote(package)), call. = FALSE, domain = NA) 1: library(GO.db) sessionInfo()R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] BiocInstaller_1.16.2 RSQLite_1.0.0DBI_0.3.1 AnnotationDbi_1.28.2 [5] GenomeInfoDb_1.2.5 IRanges_2.0.1S4Vectors_0.4.0 GEOquery_2.32.0 [9] Biobase_2.26.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2 colorspace_1.2-6 stringr_0.6.2 [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2 digest_0.6.8 [11] reshape2_1.4.1 ggplot2_1.0.1bitops_1.0-6 RCurl_1.95-4.5 scales_0.2.4 [16] XML_3.98-1.1 proto_0.3-10 Are there any way to fix this? -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3
Yes, I did the upgrading of Bioconductor as well, but the result was the same: library(BiocInstaller, lib.loc=~/Rlibs)Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help biocLite()BioC_mirror: http://bioconductor.orgUsing Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.2.0.Old packages: 'manipulate'Update all/some/none? [a/s/n]: n library(GO.db)Загрузка требуемого пакета: AnnotationDbiЗагрузка требуемого пакета: stats4Загрузка требуемого пакета: GenomeInfoDbЗагрузка требуемого пакета: S4VectorsЗагрузка требуемого пакета: IRanges Присоединяю пакет: ‘AnnotationDbi’ The following object is masked from ‘package:GenomeInfoDb’: species Загрузка требуемого пакета: DBIError : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ 2015-04-18 0:11 GMT+03:00 Dan Tenenbaum dtene...@fredhutch.org: - Original Message - From: Sergei Ryazansky s.ryazan...@gmail.com To: bioc-devel@r-project.org Sent: Friday, April 17, 2015 1:53:41 PM Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Hello everyone, after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and org.Hs.eg.db are failed to load (sorry for non-english environment): library(GO.db)Error : .onLoad не удалось в loadNamespace() для 'GO.db', подробности: вызов: ls(envir, all.names = TRUE) ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка: не удалась загрузка пакета или пространства имен для ‘GO.db’ traceback()2: stop(gettextf(package or namespace load failed for %s, sQuote(package)), call. = FALSE, domain = NA) 1: library(GO.db) sessionInfo()R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] BiocInstaller_1.16.2 RSQLite_1.0.0DBI_0.3.1 AnnotationDbi_1.28.2 [5] GenomeInfoDb_1.2.5 IRanges_2.0.1S4Vectors_0.4.0 GEOquery_2.32.0 [9] Biobase_2.26.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2 colorspace_1.2-6 stringr_0.6.2 [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2 digest_0.6.8 [11] reshape2_1.4.1 ggplot2_1.0.1bitops_1.0-6 RCurl_1.95-4.5 scales_0.2.4 [16] XML_3.98-1.1 proto_0.3-10 Are there any way to fix this? After you upgrade to R-3.2.0 you need to upgrade all your packages with: library(BiocInstaller) biocLite() Dan -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- *Sincerely,* *Sergei Ryazansky, PhD* *IMG RAS, Moscow* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] scanBam() segfault error
On 04/17/2015 08:59 AM, Leonard Goldstein wrote:
Hi all,
I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, please let me know. Many thanks for
Probably a BAM file would be a big help... Thanks, Martin
your help.
Leonard
sessionInfo()
R Under development (unstable) (2014-11-04 r66932)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rsamtools_1.19.54 Biostrings_2.35.13XVector_0.7.4
[4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20 IRanges_2.1.45
[7] S4Vectors_0.5.23 BiocGenerics_0.13.11
loaded via a namespace (and not attached):
[1] bitops_1.0-6compiler_3.2.0 tools_3.2.0 zlibbioc_1.13.3
gr - GRanges(16, IRanges(13173149, 15234449), +)
file - BamFile(file, asMates = TRUE)
param - ScanBamParam(what = scanBamWhat(), which = gr)
tmp - scanBam(file = file, param = param)
*** caught segfault ***
address 0x14538b1e, cause 'memory not mapped'
Traceback:
1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter, ...)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch({.Call(func, .extptr(file), space, flag, simpleCigar,
tagFilter, ...)}, error = function(err) {
stop(conditionMessage(err), \n f\
ile: , path(file), \n index: , index(file))})
6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
param = param)
7: scanBam(file = file, param = param)
8: scanBam(file = file, param = param)
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Re: [Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle
Sorry, I was confused. You're right, there's not much point in keeping it
compressed.
On Fri, Apr 17, 2015 at 10:14 AM, Hervé Pagès hpa...@fredhutch.org wrote:
On 04/17/2015 10:00 AM, Michael Lawrence wrote:
Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.
Not sure what you mean. Can you give an example?
H.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Hi,
I think we should just expand the Rle internally. That will produce
a numeric vector of the length of the GRanges i.e. it will be the
same size as the start and end components of the GRanges object
itself.
No big deal at all.
I'll make that change.
H.
On 04/17/2015 09:00 AM, Michael Lawrence wrote:
Ideally it should be supported, but it would take some work as
the coverage
stuff is all in C. Could you give more details on your use case?
For
example, if you already have a range for every position on the
chromosome,
you could just extract the score column. I'm guessing it's more
complicated
than that. If the zeros are the problem, you could just subset
the GRanges
to remove the ranges with zero score, and then coerce the score
to numeric
before calling coverage.
Michael
2015-04-17 8:00 GMT-07:00 Philip Lijnzaad
p.lijnz...@umcutrecht.nl mailto:p.lijnz...@umcutrecht.nl:
Dear all, I'm puzzled by the following behaviour:
Given
n - 10
gr - GRanges(seqnames=Rle('A', n),
ranges=IRanges(1:n, width=1),
score=Rle(5,n))
If I do
coverage(gr,weight='score')
I get
Error in .normarg_shift_or_weight(weight, weight, x) :
'weight' must be a numeric vector, a single string,
or a list-like
object
Surely 'score' should be allowed to be an Rle? Especially
given the
fact that the return value of coverage(x,weight=score)
when score is
plain numeric vector is always an Rle ! Is this the expected
behaviour?
If so, I would argue that violates the principle of least
suprise :-)
The background to this is that I do numerical analysis on
derived
numerical data along my chromosomes. It contains many
contiguous zeroes so it would be wasteful to cast
everything down using as.numeric().
This is R version 3.01 on x86_64 Linux, Bioconductor version
2.13,
package.version(IRanges)
[1] 1.20.7
package.version(GenomicRanges)
[1] 1.14.4
Regards,
Philip
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(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
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[Bioc-devel] scanBam() segfault error
Hi all,
I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, please let me know. Many thanks for
your help.
Leonard
sessionInfo()
R Under development (unstable) (2014-11-04 r66932)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rsamtools_1.19.54 Biostrings_2.35.13XVector_0.7.4
[4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20 IRanges_2.1.45
[7] S4Vectors_0.5.23 BiocGenerics_0.13.11
loaded via a namespace (and not attached):
[1] bitops_1.0-6compiler_3.2.0 tools_3.2.0 zlibbioc_1.13.3
gr - GRanges(16, IRanges(13173149, 15234449), +)
file - BamFile(file, asMates = TRUE)
param - ScanBamParam(what = scanBamWhat(), which = gr)
tmp - scanBam(file = file, param = param)
*** caught segfault ***
address 0x14538b1e, cause 'memory not mapped'
Traceback:
1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter, ...)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch({.Call(func, .extptr(file), space, flag, simpleCigar,
tagFilter, ...)}, error = function(err) {
stop(conditionMessage(err), \n f\
ile: , path(file), \n index: , index(file))})
6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
param = param)
7: scanBam(file = file, param = param)
8: scanBam(file = file, param = param)
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