Hi, and sorry for the delay. 1. Yes, it could certainly be that the problem was introduced recently. More precisely, in aroma.affymetrix 3.0.0 (January 2016), I added support for parallel processing via futures. Following your traceback, the error is related but not due to this new code. Thus, if you say things worked with aroma.affymetrix (< 3.0.0) but now you get this error, your observation is valid.
2. For troubleshooting, are you using any of the parallel processing features of aroma.affymetrix, cf. http://www.aroma-project.org/howtos/parallel_processing/? If you don't know or you don't set anything explicitly, the default behavior is sequential processing (as in the past). 3. For troubleshooting, are you running this on a local machine and / or are you on a shared file system (e.g. NFS)? The fact that you have a /scratch/ suggests to me that you're on a shared file system and possibly even on a compute cluster. Any details on this will help understand the problem. 4. I don't think it should matter, but it could be worth updating to the most recent version of R (3.3.1), since R 3.2.1 is rather old. 5. Now to the error itself: It's not fully clear to me why this occurs. Your answers above will help me rule out a few things. I don't think it's an issue with the aroma.affymetrix package, the future package, or any of the dependent packages. The error occurs within R and the base package itself; it's when base::installed.packages() [https://github.com/wch/r-source/blob/tags/R-3-2-1/src/library/utils/R/packages.R#L590-L604] is called. My best guess this far is that there's some kind of delay when R creates tempdir() internally and it actually appears as available to R. We've seen this type of things on NFS *across* compute nodes in the past and this is a "feature" of NFS and has little to do with R itself. /Henrik On Thu, Jul 14, 2016 at 9:34 AM, Thomas Grombacher <thomas.grombac...@merckgroup.com> wrote: > Dear Henrik, > Yes this seems obvious. I tried again, but the error remained. Also the TEMP > directory for writing is world rwx and has plenty of space left. > However the directory where the gzip file should be located does not exist: > '/scratch/tmp/RtmpwSx59C > > I have manually generated the '/scratch/tmp/RtmpwSx59C' directory. With that > the 'process(fln, verbose=verbose)' runs now. So it seems that the > generation/selection of the TMP directory for writing/reading is causing the > error. > > Here is the output from traceback() > >> traceback() > 19: gzfile(file, mode) > 18: saveRDS(list(base = base, value = ret0), dest) > 17: installed.packages() > 16: findBasePkgs() > 15: match(x, table, nomatch = 0L) > 14: pkgs %in% findBasePkgs() > 13: isBasePkgs(environmentName(where[[name]])) > 12: cleanup.Globals(globals) > 11: cleanup(globals) > 10: getGlobalsAndPackages(expr, envir = envir, tweak = tweak, resolve = > resolve, > persistent = persistent) > 9: exportGlobals(expr, envir = envir, target = NULL, tweak = tweakExpression, > resolve = TRUE) > 8: evaluator(expr, envir = envir, substitute = FALSE, ...) > 7: (function (expr, envir = parent.frame(), substitute = TRUE, evaluator = > plan(), > ...) > { > if (substitute) > expr <- substitute(expr) > if (!is.function(evaluator)) { > stop("Argument 'evaluator' must be a function: ", > typeof(evaluator)) > } > future <- evaluator(expr, envir = envir, substitute = FALSE, > ...) > if (!inherits(future, "Future")) { > stop("Argument 'evaluator' specifies a function that does not > return a Future object: ", > paste(sQuote(class(future)), collapse = ", ")) > } > future > })({ > verbose && enter(verbose, "Getting theta estimates") > theta <- extractTheta(ce, units = cellMatrixMap, drop = FALSE, > verbose = less(verbose, 5)) > verbose && str(verbose, theta) > verbose && summary(verbose, theta) > verbose && exit(verbose) > verbose && enter(verbose, "Calculating total signals") > if (ncol(theta) > 1) { > y <- theta > y[is.na(y)] <- 0 > for (cc in 2:ncol(y)) { > y[, 1] <- y[, 1] + y[, cc] > } > y <- y[, 1, drop = TRUE] > } > else { > y <- theta[, 1, drop = TRUE] > } > verbose && cat(verbose, "Total thetas:") > verbose && str(verbose, y) > verbose && exit(verbose) > verbose && enter(verbose, "Normalizing log2 signals") > if (shift != 0) > y <- y + shift > y <- log2(y) > verbose && cat(verbose, "Log2 signals:") > verbose && str(verbose, y) > yN <- .normalizeFragmentLength(y, fragmentLengths = fl, targetFcns = > targetFcns, > subsetToFit = subset, onMissing = onMissing, ...) > verbose && cat(verbose, "Normalized log2 signals:") > verbose && summary(verbose, yN) > rho <- y - yN > y <- yN <- NULL > rho <- 2^rho > verbose && cat(verbose, "Normalization scale factors:") > verbose && summary(verbose, rho) > stopifnot(length(rho) == nrow(theta)) > ok <- which(is.finite(rho)) > verbose && str(verbose, ok) > theta[ok, ] <- theta[ok, ]/rho[ok] > ok <- rho <- NULL > verbose && cat(verbose, "Normalized thetas:") > verbose && str(verbose, theta) > verbose && summary(verbose, theta) > verbose && exit(verbose) > verbose && enter(verbose, "Creating CEL file for results, if missing") > isFile <- isFile(pathname) > pathnameT <- pushTemporaryFile(pathname, isFile = isFile, > verbose = verbose) > ceN <- createFrom(ce, filename = pathnameT, path = NULL, > verbose = less(verbose)) > verbose && exit(verbose) > if (inherits(ce, "SnpChipEffectFile")) { > ceN$mergeStrands <- ce$mergeStrands > if (inherits(ce, "CnChipEffectFile")) { > ceN$combineAlleles <- ce$combineAlleles > } > } > setCdf(ceN, cdf) > verbose && enter(verbose, "Storing normalized signals") > ok <- which(is.finite(cellMatrixMap)) > cells <- cellMatrixMap[ok] > data <- theta[ok] > ok <- theta <- NULL > verbose2 <- -as.integer(verbose) - 5 > pathnameN <- getPathname(ceN) > .updateCel(pathnameN, indices = cells, intensities = data, > verbose = verbose2) > cells <- data <- ceN <- NULL > verbose && exit(verbose) > popTemporaryFile(pathnameT, verbose = verbose) > dfZ <- getChecksumFile(pathname) > gc <- gc() > verbose && print(verbose, gc) > pathname > }, envir = <environment>) > 6: do.call(future::future, args = future.args, envir = assign.env) > 5: futureAssign(name, expr, envir = envir, assign.env = assign.env, > substitute = FALSE) > 4: futureAssignInternal(target, expr, envir = envir, substitute = FALSE) > 3: res[[kk]] %<=% { > verbose && enter(verbose, "Getting theta estimates") > theta <- extractTheta(ce, units = cellMatrixMap, drop = FALSE, > verbose = less(verbose, 5)) > verbose && str(verbose, theta) > verbose && summary(verbose, theta) > verbose && exit(verbose) > verbose && enter(verbose, "Calculating total signals") > if (ncol(theta) > 1) { > y <- theta > y[is.na(y)] <- 0 > for (cc in 2:ncol(y)) { > y[, 1] <- y[, 1] + y[, cc] > } > y <- y[, 1, drop = TRUE] > } > else { > y <- theta[, 1, drop = TRUE] > } > verbose && cat(verbose, "Total thetas:") > verbose && str(verbose, y) > verbose && exit(verbose) > verbose && enter(verbose, "Normalizing log2 signals") > if (shift != 0) > y <- y + shift > y <- log2(y) > verbose && cat(verbose, "Log2 signals:") > verbose && str(verbose, y) > yN <- .normalizeFragmentLength(y, fragmentLengths = fl, targetFcns = > targetFcns, > subsetToFit = subset, onMissing = onMissing, ...) > verbose && cat(verbose, "Normalized log2 signals:") > verbose && summary(verbose, yN) > rho <- y - yN > y <- yN <- NULL > rho <- 2^rho > verbose && cat(verbose, "Normalization scale factors:") > verbose && summary(verbose, rho) > stopifnot(length(rho) == nrow(theta)) > ok <- which(is.finite(rho)) > verbose && str(verbose, ok) > theta[ok, ] <- theta[ok, ]/rho[ok] > ok <- rho <- NULL > verbose && cat(verbose, "Normalized thetas:") > verbose && str(verbose, theta) > verbose && summary(verbose, theta) > verbose && exit(verbose) > verbose && enter(verbose, "Creating CEL file for results, if missing") > isFile <- isFile(pathname) > pathnameT <- pushTemporaryFile(pathname, isFile = isFile, > verbose = verbose) > ceN <- createFrom(ce, filename = pathnameT, path = NULL, > verbose = less(verbose)) > verbose && exit(verbose) > if (inherits(ce, "SnpChipEffectFile")) { > ceN$mergeStrands <- ce$mergeStrands > if (inherits(ce, "CnChipEffectFile")) { > ceN$combineAlleles <- ce$combineAlleles > } > } > setCdf(ceN, cdf) > verbose && enter(verbose, "Storing normalized signals") > ok <- which(is.finite(cellMatrixMap)) > cells <- cellMatrixMap[ok] > data <- theta[ok] > ok <- theta <- NULL > verbose2 <- -as.integer(verbose) - 5 > pathnameN <- getPathname(ceN) > .updateCel(pathnameN, indices = cells, intensities = data, > verbose = verbose2) > cells <- data <- ceN <- NULL > verbose && exit(verbose) > popTemporaryFile(pathnameT, verbose = verbose) > dfZ <- getChecksumFile(pathname) > gc <- gc() > verbose && print(verbose, gc) > pathname > } > 2: process.FragmentLengthNormalization(fln, verbose = verbose) > 1: process(fln, verbose = verbose) > > -----Ursprüngliche Nachricht----- > Von: aroma-affymetrix@googlegroups.com > [mailto:aroma-affymetrix@googlegroups.com] Im Auftrag von Henrik Bengtsson > Gesendet: Mittwoch, 13. Juli 2016 17:45 > An: aroma-affymetrix <aroma-affymetrix@googlegroups.com> > Betreff: Re: [aroma.affymetrix] troubles in doing PCR fragment length > normalization AROMA3.0 > > That looks like a hiccup in the file system or something. Did you try again? > > Also, if the error remains, please report what traceback() outputs (as the > first command after you get the error). > > /Henrik > > On Wed, Jul 13, 2016 at 4:19 AM, <thomas.grombac...@merckgroup.com> wrote: >> Hello, >> >> I have used the standard pipeline for SNP6 CEL files described in the >> CRMAv2 vignette. I did run the pipeline before several times, without any >> issue. >> Now, the fragment length normalization step failed with an error: >> >> Error in gzfile(file, mode) : cannot open the connection >> >> I am not clear where this error comes from. >> Any support or idea is welcome. >> >> Best regards, >> Thomas >> >> My sessionInfo: >> >>> sessionInfo() >> >> R version 3.2.1 (2015-06-18) >> >> 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-8 LC_COLLATE=en_US.UTF-8 >> >> [5] LC_MONETARY=en_US.UTF-8 LC_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] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> >> [1] aroma.light_3.0.0 aroma.affymetrix_3.0.0 aroma.core_3.0.0 >> >> [4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0 >> >> [7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1 >> >> loaded via a namespace (and not attached): >> >> [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0 >> >> [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1 >> >> [9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0 >> >> [13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0 >> >> >> The full output of the process(fln, verbose=verbose) function: >> >>> cesN <- process(fln, verbose=verbose) >> >> >> 20160713 12:50:05|Normalizing set for PCR fragment-length effects... >> >> >> 20160713 12:51:07| Identifying SNP and CN units... >> >> >> types >> >> >> 1 2 5 >> >> >> 621 934968 945826 >> >> >> 20160713 12:51:09| subsetToUpdate: >> >> >> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ... >> >> >> 20160713 12:51:09| Identifying SNP and CN units...done >> >> >> 20160713 12:51:09| Retrieving SNP information annotations... >> >> >> UflSnpInformation: >> >> >> Name: GenomeWideSNP_6 >> >> >> Tags: Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1 >> 9,dbSNP137,HB20140118.ufl >> >> >> File size: 7.18 MiB (7526422 bytes) >> >> >> RAM: 0.00 MB >> >> >> Chip type: GenomeWideSNP_6,Full >> >> >> Number of enzymes: 2 >> >> >> 20160713 12:51:10| Retrieving SNP information annotations...done >> >> >> 20160713 12:51:10| Identifying the subset used to fit normalization >> function(s)... >> >> >> 20160713 12:51:10| Identifying units that are SNP and CN probes... >> >> >> UflSnpInformation: >> >> >> Name: GenomeWideSNP_6 >> >> >> Tags: Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1 >> 9,dbSNP137,HB20140118.ufl >> >> >> File size: 7.18 MiB (7526422 bytes) >> >> >> RAM: 0.00 MB >> >> >> Chip type: GenomeWideSNP_6,Full >> >> >> Number of enzymes: 2 >> >> >> 20160713 12:51:10| Identifying SNPs and CN probes... >> >> >> types >> >> >> 1 2 5 >> >> >> 621 934968 945826 >> >> >> 20160713 12:51:11| units: >> >> >> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ... >> >> >> 20160713 12:51:11| Identifying SNPs and CN probes...done >> >> >> 20160713 12:51:11| Identify subset of units from genome information... >> >> >> 20160713 12:51:11| subsetToFit: -XY >> >> >> UgpGenomeInformation: >> >> >> Name: GenomeWideSNP_6 >> >> >> Tags: Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1 >> 9,dbSNP137,HB20140118.ugp >> >> >> File size: 8.97 MiB (9407882 bytes) >> >> >> RAM: 0.00 MB >> >> >> Chip type: GenomeWideSNP_6,Full >> >> >> 20160713 12:51:18| Units to exclude: >> >> >> int [1:96544] 61101 61102 61103 61104 61105 61106 61107 61108 61109 >> 61110 ... >> >> >> 20160713 12:51:19| Units to include: >> >> >> int [1:1784871] 1 2 3 4 5 6 7 8 9 10 ... >> >> >> 20160713 12:51:19| Identify subset of units from genome >> information...done >> >> >> 20160713 12:51:19| Reading fragment lengths... >> >> >> 20160713 12:51:19| Reading and filtering fragment lengths... >> >> >> 20160713 12:51:19| Reading fragment lengths... >> >> >> UflSnpInformation: >> >> >> Name: GenomeWideSNP_6 >> >> >> Tags: Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1 >> 9,dbSNP137,HB20140118.ufl >> >> >> File size: 7.18 MiB (7526422 bytes) >> >> >> RAM: 0.00 MB >> >> >> Chip type: GenomeWideSNP_6,Full >> >> >> Number of enzymes: 2 >> >> >> 20160713 12:51:26| Summary of non-filtered fragment lengths: >> >> >> int [1:1880794, 1:2] 395 4056 633 831 970 1508 4025 4557 3779 420 ... >> >> >> V1 V2 >> >> >> Min. : 7.0 Min. : 7 >> >> >> 1st Qu.: 430.0 1st Qu.: 628 >> >> >> Median : 676.0 Median : 1078 >> >> >> Mean : 915.2 Mean : 1410 >> >> >> 3rd Qu.: 970.0 3rd Qu.: 1730 >> >> >> Max. :32767.0 Max. :32767 >> >> >> NA's :2279 NA's :447301 >> >> >> 20160713 12:51:27| Reading fragment lengths...done >> >> >> 20160713 12:51:27| Filtering fragment lengths... >> >> >> 20160713 12:51:27| Filtering fragment lengths...done >> >> >> 20160713 12:51:27| Reading and filtering fragment lengths...done >> >> >> 20160713 12:51:27| Reading fragment lengths...done >> >> >> 20160713 12:51:28| Identifying units that are SNP and CN probes...done >> >> >> int [1:1784250] 622 623 624 625 626 627 628 629 630 631 ... >> >> >> 20160713 12:51:28| Identifying the subset used to fit normalization >> function(s)...done >> >> >> 20160713 12:51:28| Shift: 0 >> >> >> 20160713 12:51:28| onMissing: median >> >> >> 20160713 12:51:28| Array #1 of 1213 >> ('ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002')... >> >> >> 20160713 12:51:28| Reading and filtering fragment lengths... >> >> >> 20160713 12:51:28| Reading fragment lengths... >> >> >> UflSnpInformation: >> >> >> Name: GenomeWideSNP_6 >> >> >> Tags: Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1 >> 9,dbSNP137,HB20140118.ufl >> >> >> File size: 7.18 MiB (7526422 bytes) >> >> >> RAM: 14.36 MB >> >> >> Chip type: GenomeWideSNP_6,Full >> >> >> Number of enzymes: 2 >> >> >> 20160713 12:51:33| Summary of non-filtered fragment lengths: >> >> >> int [1:1880794, 1:2] 395 4056 633 831 970 1508 4025 4557 3779 420 ... >> >> >> V1 V2 >> >> >> Min. : 7.0 Min. : 7 >> >> >> 1st Qu.: 430.0 1st Qu.: 628 >> >> >> Median : 676.0 Median : 1078 >> >> >> Mean : 915.2 Mean : 1410 >> >> >> 3rd Qu.: 970.0 3rd Qu.: 1730 >> >> >> Max. :32767.0 Max. :32767 >> >> >> NA's :2279 NA's :447301 >> >> >> 20160713 12:51:37| Reading fragment lengths...done >> >> >> 20160713 12:51:37| Filtering fragment lengths... >> >> >> 20160713 12:51:37| Filtering fragment lengths...done >> >> >> 20160713 12:51:37| Reading and filtering fragment lengths...done >> >> >> V1 V2 >> >> >> Min. : 7.0 Min. : 7 >> >> >> 1st Qu.: 430.0 1st Qu.: 628 >> >> >> Median : 676.0 Median : 1078 >> >> >> Mean : 915.2 Mean : 1410 >> >> >> 3rd Qu.: 970.0 3rd Qu.: 1730 >> >> >> Max. :32767.0 Max. :32767 >> >> >> NA's :2279 NA's :447301 >> >> >> int [1:1784250] 1 2 3 4 5 6 7 8 9 10 ... >> >> >> UflSnpInformation: >> >> >> Name: GenomeWideSNP_6 >> >> >> Tags: Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118 >> >> >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1 >> 9,dbSNP137,HB20140118.ufl >> >> >> File size: 7.18 MiB (7526422 bytes) >> >> >> RAM: 14.36 MB >> >> >> Chip type: GenomeWideSNP_6,Full >> >> >> Number of enzymes: 2 >> >> >> 20160713 12:51:40| Setting up predefined target functions... >> >> >> 20160713 12:51:40| Target type: zero >> >> >> 20160713 12:51:40| Setting up predefined target functions...done >> >> >> 20160713 12:51:40| Getting cell matrix map... >> >> >> 'UnitGroupCellMatrixMap' int [1:1880794, 1:2] 622 624 626 628 630 632 >> 634 >> 636 638 640 ... >> >> >> 20160713 12:51:44| Getting cell matrix map...done >> >> >> Error in gzfile(file, mode) : cannot open the connection >> >> >> In addition: Warning message: >> >> >> In gzfile(file, mode) : >> >> >> cannot open compressed file >> '/scratch/tmp/RtmpwSx59C/libloc_178_ccc298d560fce69b.rds', probable >> reason 'No such file or directory' >> >> >> 20160713 12:51:45| Array #1 of 1213 >> ('ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002')...done >> >> >> 20160713 12:51:45|Normalizing set for PCR fragment-length >> effects...done >> >> >> >> >> >> -- >> -- >> When reporting problems on aroma.affymetrix, make sure 1) to run the >> latest version of the package, 2) to report the output of >> sessionInfo() and traceback(), and 3) to post a complete code example. >> >> >> You received this message because you are subscribed to the Google >> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ >> >> --- >> You received this message because you are subscribed to the Google >> Groups "aroma.affymetrix" group. >> To unsubscribe from this group and stop receiving emails from it, send >> an email to aroma-affymetrix+unsubscr...@googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to 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You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
