search

hansenlab / minfi

Devel repository for minfi
58 stars 70 forks source link

Error in read.metharray(basenames = commonFiles, extended = extended, : [read.metharray] Trying to parse different IDAT files, of different size and type. #195

Closed boseb closed 3 years ago

boseb commented 4 years ago

Hi, I am having error while trying to read methylation data using minfi:

getGEOSuppFiles("GSE122126")
untar("GSE122126/GSE122126_RAW.tar", exdir = "GSE122126/idat")

idatFiles <- list.files("GSE122126/idat", pattern = "idat.gz$", full = TRUE)
sapply(idatFiles, gunzip, overwrite = TRUE)

rgSet <- read.metharray.exp("GSE122126/idat/",force = TRUE,recursive = T)

### **Error in read.metharray(basenames = commonFiles, extended = extended,  : 
  [read.metharray] Trying to parse different IDAT files, of different size and type.**

> session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.0 (2019-04-26)
 os       CentOS Linux 7 (Core)       
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Chicago             
 date     2019-12-06                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 !  package                                       * version    date       lib source                                          
    acepack                                         1.4.1      2016-10-29 [1] CRAN (R 3.6.0)                                  
    ade4                                            1.7-13     2018-08-31 [1] CRAN (R 3.6.0)                                  
 P  annotate                                        1.62.0     2019-05-02 [2] Bioconductor                                    
 P  AnnotationDbi                                   1.46.1     2019-08-20 [2] Bioconductor                                    
    AnnotationHub                                 * 2.14.5     2019-03-14 [1] Bioconductor                                    
 P  ape                                             5.3        2019-03-17 [2] CRAN (R 3.6.0)                                  
 P  aroma.light                                     3.14.0     2019-05-02 [2] Bioconductor                                    
    askpass                                         1.1        2019-01-13 [1] CRAN (R 3.6.0)                                  
    assertthat                                      0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                                  
    backports                                       1.1.5      2019-10-02 [1] CRAN (R 3.6.0)                                  
    base64                                          2.0        2016-05-10 [1] CRAN (R 3.6.0)                                  
    base64enc                                       0.1-3      2015-07-28 [1] CRAN (R 3.6.0)                                  
    BBmisc                                        * 1.11       2019-09-12 [1] Github (berndbischl/BBmisc@a5a4e45)             
    bbmle                                           1.0.20     2017-10-30 [1] CRAN (R 3.6.0)                                  
    beanplot                                        1.2        2014-09-19 [1] CRAN (R 3.6.0)                                  
    beeswarm                                        0.2.3      2016-04-25 [1] CRAN (R 3.6.0)                                  
 P  bibtex                                          0.4.2      2017-06-30 [2] CRAN (R 3.5.2)                                  
    binr                                          * 1.1        2015-03-10 [2] CRAN (R 3.6.0)                                  
    Biobase                                       * 2.44.0     2019-05-02 [1] Bioconductor                                    
 V  BiocFileCache                                   1.6.0      2019-05-02 [1] Bioconductor                                    
    BiocGenerics                                  * 0.30.0     2019-05-02 [1] Bioconductor                                    
 VP BiocManager                                   * 1.30.9     2019-11-16 [2] CRAN (R 3.6.0)                                  
    BiocNeighbors                                   1.2.0      2019-05-02 [1] Bioconductor                                    
 P  BiocParallel                                  * 1.18.1     2019-08-06 [2] Bioconductor                                    
    BiocSingular                                    1.0.0      2019-05-02 [1] Bioconductor                                    
    BiocStyle                                       2.12.0     2019-05-02 [1] Bioconductor                                    
    bioDist                                         1.56.0     2019-05-02 [1] Bioconductor                                    
 P  biomaRt                                       * 2.40.5     2019-10-01 [2] Bioconductor                                    
 P  Biostrings                                    * 2.52.0     2019-05-02 [2] Bioconductor                                    
 P  bit                                             1.1-14     2018-05-29 [2] CRAN (R 3.6.0)                                  
 P  bit64                                           0.9-7      2017-05-08 [2] CRAN (R 3.6.0)                                  
    bitops                                          1.0-6      2013-08-17 [1] CRAN (R 3.6.0)                                  
 P  blob                                            1.2.0      2019-07-09 [2] CRAN (R 3.6.0)                                  
    boot                                            1.3-22     2019-04-02 [3] CRAN (R 3.6.0)                                  
 P  broom                                           0.5.2      2019-04-07 [2] CRAN (R 3.6.0)                                  
    bumphunter                                    * 1.26.0     2019-05-02 [1] Bioconductor                                    
    callr                                           3.3.2      2019-09-22 [1] CRAN (R 3.6.0)                                  
    caret                                         * 6.0-84     2019-04-27 [1] CRAN (R 3.6.0)                                  
 V  caTools                                         1.17.1.2   2019-11-30 [1] CRAN (R 3.6.0)                                  
    CePa                                          * 0.6        2018-06-04 [1] CRAN (R 3.5.2)                                  
    checkmate                                       1.9.4      2019-07-04 [1] CRAN (R 3.6.0)                                  
    CHETAH                                        * 1.0.5      2019-09-19 [1] Bioconductor                                    
 P  chron                                           2.3-54     2019-08-26 [2] CRAN (R 3.6.0)                                  
 P  circlize                                        0.4.8      2019-09-08 [2] CRAN (R 3.6.0)                                  
    class                                           7.3-15     2019-01-01 [3] CRAN (R 3.6.0)                                  
    cli                                             1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                                  
 P  clue                                            0.3-57     2019-02-25 [2] CRAN (R 3.6.0)                                  
    cluster                                       * 2.0.8      2019-04-05 [3] CRAN (R 3.6.0)                                  
    clusterSim                                    * 0.48-1     2019-11-05 [1] CRAN (R 3.6.0)                                  
    coda                                            0.19-3     2019-07-05 [1] CRAN (R 3.6.0)                                  
    codetools                                       0.2-16     2018-12-24 [3] CRAN (R 3.6.0)                                  
 P  colorspace                                      1.4-1      2019-03-18 [2] CRAN (R 3.5.2)                                  
 P  ComplexHeatmap                                  2.0.0      2019-05-02 [2] Bioconductor                                    
 P  ConsensusClusterPlus                            1.48.0     2019-05-02 [2] Bioconductor                                    
    coop                                            0.6-2      2019-04-22 [1] CRAN (R 3.6.0)                                  
    corrplot                                        0.84       2017-10-16 [1] CRAN (R 3.6.0)                                  
    cowplot                                         1.0.0      2019-07-11 [1] CRAN (R 3.6.0)                                  
    crayon                                          1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                                  
    crosstalk                                       1.0.0      2016-12-21 [1] CRAN (R 3.5.2)                                  
    curl                                            4.2        2019-09-24 [1] CRAN (R 3.6.0)                                  
 P  data.table                                    * 1.12.6     2019-10-18 [2] CRAN (R 3.6.0)                                  
 P  DBI                                             1.0.0      2018-05-02 [2] CRAN (R 3.6.0)                                  
 V  dbplyr                                          1.3.0      2019-06-17 [1] CRAN (R 3.6.0)                                  
    deconvSeq                                     * 0.1.2      2019-11-17 [1] Github (rosedu1/deconvSeq@b4de0d1)              
    DelayedArray                                  * 0.10.0     2019-05-02 [1] Bioconductor                                    
    DelayedMatrixStats                              1.6.1      2019-09-08 [1] Bioconductor                                    
 V  dendextend                                      1.12.0     2019-12-02 [1] CRAN (R 3.6.0)                                  
    DEoptimR                                        1.0-8      2016-11-19 [1] CRAN (R 3.6.0)                                  
    desc                                            1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                                  
 P  DESeq                                           1.36.0     2019-05-02 [2] Bioconductor                                    
    devtools                                      * 2.2.1      2019-09-24 [1] CRAN (R 3.6.0)                                  
 P  digest                                          0.6.22     2019-10-21 [2] CRAN (R 3.6.0)                                  
 P  dnet                                          * 1.1.5      2019-10-18 [2] CRAN (R 3.6.0)                                  
 P  doParallel                                    * 1.0.15     2019-08-02 [2] CRAN (R 3.6.0)                                  
    doRNG                                           1.7.1      2018-06-22 [1] CRAN (R 3.6.0)                                  
 P  downloader                                      0.4        2015-07-09 [2] CRAN (R 3.6.0)                                  
    dplyr                                           0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                                  
    dqrng                                           0.2.1      2019-05-17 [1] CRAN (R 3.6.0)                                  
    dynamicTreeCut                                * 1.63-1     2016-03-11 [1] CRAN (R 3.6.0)                                  
 V  e1071                                           1.7-2      2019-11-26 [1] CRAN (R 3.6.0)                                  
 P  EDASeq                                          2.18.0     2019-05-02 [2] Bioconductor                                    
    EDec                                          * 0.9        2019-11-29 [1] Github (BRL-BCM/EDec@87b47f0)                   
    EDecExampleData                               * 0.9        2019-11-29 [1] Github (BRL-BCM/EDecExampleData@7e80abd)        
 P  edgeR                                         * 3.26.8     2019-09-01 [2] Bioconductor                                    
    ellipsis                                        0.3.0      2019-09-20 [1] CRAN (R 3.6.0)                                  
    emdbook                                         1.3.11     2019-02-12 [1] CRAN (R 3.6.0)                                  
    evaluate                                        0.14       2019-05-28 [1] CRAN (R 3.6.0)                                  
    ExperimentHub                                 * 1.8.0      2018-10-30 [1] Bioconductor                                    
    fastcluster                                   * 1.1.25     2018-06-07 [1] CRAN (R 3.6.0)                                  
    fastseg                                         1.30.0     2019-05-02 [1] Bioconductor                                    
    FateID                                          0.1.9      2019-09-21 [1] CRAN (R 3.6.0)                                  
    fit.models                                      0.5-14     2017-04-06 [1] CRAN (R 3.6.0)                                  
    FlowSorted.Blood.450k                         * 1.22.0     2019-05-07 [1] Bioconductor                                    
    FlowSorted.Blood.EPIC                         * 1.2.0      2019-05-07 [1] Bioconductor                                    
    FNN                                             1.1.3      2019-02-15 [1] CRAN (R 3.6.0)                                  
 P  foreach                                       * 1.4.7      2019-07-27 [2] CRAN (R 3.6.0)                                  
    foreign                                         0.8-71     2018-07-20 [3] CRAN (R 3.6.0)                                  
    Formula                                         1.2-3      2018-05-03 [1] CRAN (R 3.6.0)                                  
    fs                                              1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                                  
    gdata                                           2.18.0     2017-06-06 [1] CRAN (R 3.6.0)                                  
 P  genefilter                                    * 1.66.0     2019-05-02 [2] Bioconductor                                    
 P  geneplotter                                     1.62.0     2019-05-02 [2] Bioconductor                                    
 P  generics                                        0.0.2      2018-11-29 [2] CRAN (R 3.6.0)                                  
    GenomeInfoDb                                  * 1.20.0     2019-05-02 [1] Bioconductor                                    
    GenomeInfoDbData                                1.2.1      2019-08-29 [1] Bioconductor                                    
 P  GenomicAlignments                               1.20.1     2019-06-18 [2] Bioconductor                                    
 P  GenomicFeatures                                 1.36.4     2019-07-10 [2] Bioconductor                                    
    GenomicRanges                                 * 1.36.1     2019-09-06 [1] Bioconductor                                    
    GEOquery                                      * 2.52.0     2019-05-02 [1] Bioconductor                                    
 P  GetoptLong                                      0.1.7      2018-06-10 [2] CRAN (R 3.6.0)                                  
    GGally                                          1.4.0      2018-05-17 [1] CRAN (R 3.5.2)                                  
    ggbeeswarm                                      0.6.0      2017-08-07 [1] CRAN (R 3.6.0)                                  
 P  ggplot2                                       * 3.2.1      2019-08-10 [2] CRAN (R 3.6.0)                                  
 VP ggpubr                                          0.2.3      2019-11-14 [2] CRAN (R 3.6.0)                                  
 P  ggrepel                                         0.8.1      2019-05-07 [2] CRAN (R 3.6.0)                                  
 P  ggsignif                                        0.6.0      2019-08-08 [2] CRAN (R 3.6.0)                                  
 P  ggthemes                                        4.2.0      2019-05-13 [2] CRAN (R 3.6.0)                                  
    glmnet                                        * 2.0-18     2019-05-20 [1] CRAN (R 3.6.0)                                  
 P  GlobalOptions                                   0.1.1      2019-09-30 [2] CRAN (R 3.6.0)                                  
    glue                                            1.3.1      2019-03-12 [1] CRAN (R 3.5.2)                                  
    GO.db                                           3.8.2      2019-08-29 [1] Bioconductor                                    
    gower                                           0.2.1      2019-05-14 [1] CRAN (R 3.6.0)                                  
    gplots                                        * 3.0.1.1    2019-01-27 [1] CRAN (R 3.5.2)                                  
 P  graph                                           1.62.0     2019-05-02 [2] Bioconductor                                    
 P  gridBase                                        0.4-7      2014-02-24 [2] CRAN (R 3.6.0)                                  
 P  gridExtra                                       2.3        2017-09-09 [2] CRAN (R 3.6.0)                                  
 P  gsubfn                                        * 0.7        2018-03-16 [2] CRAN (R 3.6.0)                                  
 P  gtable                                          0.3.0      2019-03-25 [2] CRAN (R 3.6.0)                                  
    gtools                                          3.8.1      2018-06-26 [1] CRAN (R 3.6.0)                                  
    HDF5Array                                       1.12.3     2019-10-15 [1] Bioconductor                                    
 VP hexbin                                        * 1.27.3     2019-11-11 [2] CRAN (R 3.6.0)                                  
 V  Hmisc                                           4.2-0      2019-11-07 [1] CRAN (R 3.6.0)                                  
 P  hms                                             0.5.2      2019-10-30 [2] CRAN (R 3.6.0)                                  
 V  htmlTable                                       1.13.1     2019-12-04 [1] CRAN (R 3.6.0)                                  
    htmltools                                       0.4.0      2019-10-04 [1] CRAN (R 3.6.0)                                  
    htmlwidgets                                     1.5.1      2019-10-08 [1] CRAN (R 3.6.0)                                  
 V  httpuv                                          1.5.1      2019-09-11 [1] CRAN (R 3.6.0)                                  
 P  httr                                            1.4.1      2019-08-05 [2] CRAN (R 3.6.0)                                  
 P  hwriter                                         1.3.2      2014-09-10 [2] CRAN (R 3.6.0)                                  
    ica                                             1.0-2      2018-05-24 [1] CRAN (R 3.6.0)                                  
    igraph                                        * 1.2.4.1    2019-04-22 [1] CRAN (R 3.6.0)                                  
    IlluminaHumanMethylation27kanno.ilmn12.hg19   * 0.6.0      2019-11-30 [1] Bioconductor                                    
    IlluminaHumanMethylation27kmanifest           * 0.4.0      2019-11-30 [1] Bioconductor                                    
    IlluminaHumanMethylation450kanno.ilmn12.hg19  * 0.6.0      2019-11-30 [1] Bioconductor                                    
    IlluminaHumanMethylation450kmanifest          * 0.4.0      2019-11-30 [1] Bioconductor                                    
    IlluminaHumanMethylationEPICanno.ilm10b4.hg19 * 0.6.0      2019-11-30 [1] Bioconductor                                    
    IlluminaHumanMethylationEPICmanifest          * 0.3.0      2019-11-30 [1] Bioconductor                                    
    illuminaio                                      0.26.0     2019-05-02 [1] Bioconductor                                    
    impute                                          1.58.0     2019-05-02 [1] Bioconductor                                    
    interactiveDisplayBase                          1.20.0     2018-10-30 [1] Bioconductor                                    
 V  ipred                                           0.9-8      2019-04-28 [1] CRAN (R 3.6.0)                                  
    IRanges                                       * 2.18.3     2019-09-24 [1] Bioconductor                                    
    irlba                                           2.3.3      2019-02-05 [1] CRAN (R 3.6.0)                                  
 P  iterators                                     * 1.0.12     2019-07-26 [2] CRAN (R 3.6.0)                                  
 V  janitor                                       * 1.1.1      2019-04-21 [1] CRAN (R 3.6.0)                                  
 P  jsonlite                                        1.6        2018-12-07 [2] CRAN (R 3.6.0)                                  
    KernSmooth                                      2.23-15    2015-06-29 [3] CRAN (R 3.6.0)                                  
 P  km.ci                                           0.5-2      2009-08-30 [2] CRAN (R 3.6.0)                                  
 P  KMsurv                                          0.1-5      2012-12-03 [2] CRAN (R 3.6.0)                                  
 VP knitr                                           1.25       2019-11-12 [2] CRAN (R 3.6.0)                                  
 V  later                                           0.8.0      2019-10-04 [1] CRAN (R 3.6.0)                                  
    lattice                                       * 0.20-38    2018-11-04 [3] CRAN (R 3.6.0)                                  
 P  latticeExtra                                    0.6-28     2016-02-09 [2] CRAN (R 3.6.0)                                  
    lava                                            1.6.6      2019-08-01 [1] CRAN (R 3.6.0)                                  
 P  lazyeval                                        0.2.2      2019-03-15 [2] CRAN (R 3.5.2)                                  
 P  lifecycle                                       0.1.0      2019-08-01 [2] CRAN (R 3.6.0)                                  
 P  limma                                         * 3.40.6     2019-07-26 [2] Bioconductor                                    
    lle                                             1.1        2012-03-21 [1] CRAN (R 3.6.0)                                  
    lme4                                            1.1-21     2019-03-05 [1] CRAN (R 3.5.2)                                  
 P  locfit                                        * 1.5-9.1    2013-04-20 [2] CRAN (R 3.6.0)                                  
    lubridate                                       1.7.4      2018-04-11 [1] CRAN (R 3.5.1)                                  
 P  maftools                                      * 2.0.16     2019-08-14 [2] Bioconductor                                    
    magrittr                                        1.5        2014-11-22 [1] CRAN (R 3.6.0)                                  
    manipulateWidget                                0.10.0     2018-06-11 [1] CRAN (R 3.6.0)                                  
    MASS                                          * 7.3-51.4   2019-03-31 [3] CRAN (R 3.6.0)                                  
 P  matlab                                          1.0.2      2014-06-24 [2] CRAN (R 3.6.0)                                  
 VP Matrix                                        * 1.2-17     2019-11-27 [3] CRAN (R 3.6.0)                                  
    matrixStats                                   * 0.55.0     2019-09-07 [1] CRAN (R 3.6.0)                                  
    mclust                                          5.4.5      2019-07-08 [1] CRAN (R 3.6.0)                                  
 P  memoise                                         1.1.0      2017-04-21 [2] CRAN (R 3.6.0)                                  
    methylKit                                       1.10.0     2019-05-02 [1] Bioconductor                                    
    mgcv                                            1.8-28     2019-03-21 [3] CRAN (R 3.6.0)                                  
    mime                                            0.7        2019-06-11 [1] CRAN (R 3.6.0)                                  
    minfi                                         * 1.30.0     2019-05-02 [1] Bioconductor                                    
    miniUI                                          0.1.1.1    2018-05-18 [1] CRAN (R 3.6.0)                                  
    minqa                                           1.2.4      2014-10-09 [1] CRAN (R 3.6.0)                                  
    mnormt                                          1.5-5      2016-10-15 [1] CRAN (R 3.6.0)                                  
    ModelMetrics                                    1.2.2      2018-11-03 [1] CRAN (R 3.6.0)                                  
    multtest                                        2.40.0     2019-05-02 [1] Bioconductor                                    
 P  munsell                                         0.5.0      2018-06-12 [2] CRAN (R 3.6.0)                                  
    mvtnorm                                         1.0-11     2019-06-19 [1] CRAN (R 3.6.0)                                  
    nlme                                          * 3.1-139    2019-04-09 [3] CRAN (R 3.6.0)                                  
    nloptr                                          1.2.1      2018-10-03 [1] CRAN (R 3.6.0)                                  
 P  NMF                                             0.21.0     2018-03-06 [2] CRAN (R 3.5.2)                                  
    nnet                                            7.3-12     2016-02-02 [3] CRAN (R 3.6.0)                                  
    nor1mix                                         1.3-0      2019-06-13 [1] CRAN (R 3.6.0)                                  
    numDeriv                                        2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0)                                  
    openssl                                         1.4.1      2019-07-18 [1] CRAN (R 3.6.0)                                  
 V  pbapply                                       * 1.4-1      2019-08-31 [1] CRAN (R 3.6.0)                                  
    pcaPP                                           1.9-73     2018-01-14 [1] CRAN (R 3.6.0)                                  
    permute                                         0.9-5      2019-03-12 [1] CRAN (R 3.6.0)                                  
    pheatmap                                        1.0.12     2019-01-04 [1] CRAN (R 3.6.0)                                  
    pillar                                          1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                                  
 V  pkgbuild                                        1.0.3      2019-10-09 [1] CRAN (R 3.6.0)                                  
    pkgconfig                                       2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                                  
    pkgload                                         1.0.2      2018-10-29 [1] CRAN (R 3.5.1)                                  
 P  pkgmaker                                        0.27       2018-05-25 [2] CRAN (R 3.5.2)                                  
    plotly                                          4.9.1      2019-11-07 [1] CRAN (R 3.6.0)                                  
 P  plyr                                          * 1.8.4      2016-06-08 [2] CRAN (R 3.5.2)                                  
 P  png                                             0.1-7      2013-12-03 [2] CRAN (R 3.6.0)                                  
    preprocessCore                                  1.46.0     2019-05-02 [1] Bioconductor                                    
 P  prettyunits                                     1.0.2      2015-07-13 [2] CRAN (R 3.5.1)                                  
    princurve                                       2.1.4      2019-05-29 [1] CRAN (R 3.6.0)                                  
    processx                                        3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                                  
 V  prodlim                                         2018.04.18 2019-11-17 [1] CRAN (R 3.6.0)                                  
 P  progress                                        1.2.2      2019-05-16 [2] CRAN (R 3.6.0)                                  
 V  promises                                        1.0.1      2019-10-04 [1] CRAN (R 3.6.0)                                  
    propr                                           4.1.6      2019-07-10 [1] CRAN (R 3.6.0)                                  
 P  proto                                         * 1.0.0      2016-10-29 [2] CRAN (R 3.6.0)                                  
    ps                                              1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                                  
    psych                                           1.8.12     2019-01-12 [1] CRAN (R 3.6.0)                                  
    purrr                                           0.3.3      2019-10-18 [1] CRAN (R 3.6.0)                                  
 V  quadprog                                      * 1.5-7      2019-11-20 [1] CRAN (R 3.6.0)                                  
    qvalue                                          2.16.0     2019-05-02 [1] Bioconductor                                    
 P  R.methodsS3                                     1.7.1      2016-02-16 [2] CRAN (R 3.6.0)                                  
 P  R.oo                                            1.23.0     2019-11-03 [2] CRAN (R 3.6.0)                                  
 VP R.utils                                         2.9.0      2019-12-05 [2] CRAN (R 3.6.0)                                  
    R2HTML                                          2.3.2      2016-06-23 [1] CRAN (R 3.6.0)                                  
 VP R6                                              2.4.0      2019-11-12 [2] CRAN (R 3.6.0)                                  
 V  RaceID                                        * 0.1.5      2019-11-21 [1] CRAN (R 3.6.0)                                  
    RaggedExperiment                                1.8.0      2019-05-02 [1] Bioconductor                                    
    randomForest                                    4.6-14     2018-03-25 [1] CRAN (R 3.6.0)                                  
    rappdirs                                        0.3.1      2016-03-28 [1] CRAN (R 3.6.0)                                  
    RCircos                                         1.2.1      2019-03-12 [1] CRAN (R 3.6.0)                                  
 P  RColorBrewer                                    1.1-2      2014-12-07 [2] CRAN (R 3.6.0)                                  
 V  Rcpp                                          * 1.0.2      2019-11-08 [1] CRAN (R 3.6.0)                                  
    RCurl                                           1.95-4.12  2019-03-04 [1] CRAN (R 3.5.2)                                  
 P  readr                                         * 1.3.1      2018-12-21 [2] CRAN (R 3.5.2)                                  
 V  recipes                                         0.1.6      2019-09-15 [1] CRAN (R 3.6.0)                                  
 P  registry                                        0.5-1      2019-03-05 [2] CRAN (R 3.6.0)                                  
    remotes                                         2.1.0      2019-06-24 [1] CRAN (R 3.6.0)                                  
    reshape                                       * 0.8.8      2018-10-23 [1] CRAN (R 3.5.1)                                  
 P  reshape2                                      * 1.4.3      2017-12-11 [2] CRAN (R 3.5.1)                                  
    reticulate                                      1.13       2019-07-24 [1] CRAN (R 3.6.0)                                  
    rgl                                             0.100.30   2019-08-19 [1] CRAN (R 3.6.0)                                  
 P  Rgraphviz                                       2.28.0     2019-05-02 [2] Bioconductor                                    
    rhdf5                                           2.28.1     2019-10-10 [1] Bioconductor                                    
    Rhdf5lib                                        1.6.3      2019-10-15 [1] Bioconductor                                    
 P  rJava                                           0.9-11     2019-03-29 [2] CRAN (R 3.6.0)                                  
 P  rjson                                           0.2.20     2018-06-08 [2] CRAN (R 3.6.0)                                  
 V  RJSONIO                                         1.3-1.2    2019-10-03 [1] CRAN (R 3.6.0)                                  
 VP rlang                                           0.4.1      2019-11-23 [2] CRAN (R 3.6.0)                                  
 V  rmarkdown                                       1.16       2019-11-27 [1] CRAN (R 3.6.0)                                  
    Rmisc                                           1.5        2013-10-22 [1] CRAN (R 3.6.0)                                  
 P  rngtools                                        1.4        2019-07-01 [2] CRAN (R 3.6.0)                                  
 V  robust                                          0.4-18     2019-07-02 [1] CRAN (R 3.6.0)                                  
 V  robustbase                                      0.93-4     2019-05-12 [1] CRAN (R 3.6.0)                                  
    ROCR                                          * 1.0-7      2015-03-26 [1] CRAN (R 3.6.0)                                  
    rpart                                           4.1-15     2019-04-12 [3] CRAN (R 3.6.0)                                  
    rprojroot                                       1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                                  
 V  rrcov                                           1.4-7      2019-11-25 [1] CRAN (R 3.6.0)                                  
 P  Rsamtools                                       2.0.3      2019-10-10 [2] Bioconductor                                    
    rslurm                                        * 0.5.0      2019-11-15 [2] CRAN (R 3.6.0)                                  
    Rsolnp                                          1.16       2015-12-28 [1] CRAN (R 3.6.0)                                  
 P  RSQLite                                       * 2.1.2      2019-07-24 [2] CRAN (R 3.6.0)                                  
    rstudioapi                                      0.10       2019-03-19 [1] CRAN (R 3.6.0)                                  
    rsvd                                            1.0.2      2019-07-29 [1] CRAN (R 3.6.0)                                  
    RTCGAToolbox                                  * 2.14.0     2019-05-02 [1] Bioconductor                                    
 P  rtracklayer                                     1.44.4     2019-09-06 [2] Bioconductor                                    
    Rtsne                                           0.15       2018-11-10 [1] CRAN (R 3.6.0)                                  
 P  rvest                                           0.3.5      2019-11-08 [2] CRAN (R 3.6.0)                                  
    S4Vectors                                     * 0.22.1     2019-09-09 [1] Bioconductor                                    
 VP scales                                        * 1.0.0      2019-11-18 [2] CRAN (R 3.6.0)                                  
    scater                                          1.12.2     2019-05-24 [1] Bioconductor                                    
    scatterplot3d                                   0.3-41     2018-03-14 [1] CRAN (R 3.6.0)                                  
    scran                                           1.12.1     2019-05-27 [1] Bioconductor                                    
    scrime                                          1.3.5      2018-12-01 [1] CRAN (R 3.6.0)                                  
 VP selectr                                         0.4-1      2019-11-20 [2] CRAN (R 3.6.0)                                  
    sessioninfo                                     1.1.1      2018-11-05 [1] CRAN (R 3.5.1)                                  
 P  shape                                           1.4.4      2018-02-07 [2] CRAN (R 3.6.0)                                  
    shiny                                           1.3.1      2019-04-12 [1] CRAN (R 3.5.2)                                  
 P  ShortRead                                       1.42.0     2019-05-02 [2] Bioconductor                                    
    siggenes                                        1.58.0     2019-05-02 [1] Bioconductor                                    
    simpleSingleCell                                1.8.0      2019-05-03 [1] Bioconductor                                    
    SingleCellExperiment                          * 1.6.0      2019-05-02 [1] Bioconductor                                    
    snowfall                                        1.84-6.1   2015-10-14 [1] CRAN (R 3.6.0)                                  
    som                                             0.3-5.1    2016-07-06 [1] CRAN (R 3.6.0)                                  
 P  sqldf                                         * 0.4-11     2017-06-28 [2] CRAN (R 3.5.1)                                  
    statmod                                         1.4.32     2019-05-29 [1] CRAN (R 3.6.0)                                  
 P  stringi                                         1.4.3      2019-03-12 [2] CRAN (R 3.5.2)                                  
 P  stringr                                       * 1.4.0      2019-02-10 [2] CRAN (R 3.6.0)                                  
    SummarizedExperiment                          * 1.14.1     2019-07-31 [1] Bioconductor                                    
 P  supraHex                                      * 1.22.0     2019-05-02 [2] Bioconductor                                    
    survival                                        2.44-1.1   2019-04-01 [3] CRAN (R 3.6.0)                                  
 P  survminer                                       0.4.6      2019-09-03 [2] CRAN (R 3.6.0)                                  
 P  survMisc                                        0.5.5      2018-07-05 [2] CRAN (R 3.5.1)                                  
 P  sva                                             3.32.1     2019-05-22 [2] Bioconductor                                    
    svdvis                                        * 0.1        2019-08-18 [1] Github (ncchung/svdvis@8a3ab56)                 
 P  TCGAbiolinks                                  * 2.13.6     2019-09-12 [2] Github (BioinformaticsFMRP/TCGAbiolinks@3fd0bce)
    TDM                                           * 0.3        2019-11-11 [2] Github (greenelab/TDM@362a1f7)                  
    testthat                                        2.2.1      2019-07-25 [1] CRAN (R 3.6.0)                                  
    tibble                                          2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                                  
 P  tidyr                                           1.0.0      2019-09-11 [2] CRAN (R 3.6.0)                                  
    tidyselect                                      0.2.5      2018-10-11 [1] CRAN (R 3.5.1)                                  
    timeDate                                        3043.102   2018-02-21 [1] CRAN (R 3.6.0)                                  
    truncnorm                                       1.0-8      2018-02-27 [1] CRAN (R 3.6.0)                                  
    umap                                            0.2.3.1    2019-08-21 [1] CRAN (R 3.6.0)                                  
    usethis                                       * 1.5.1      2019-07-04 [1] CRAN (R 3.6.0)                                  
 P  vctrs                                           0.2.0      2019-07-05 [2] CRAN (R 3.6.0)                                  
    vegan                                           2.5-6      2019-09-01 [1] CRAN (R 3.6.0)                                  
    vipor                                           0.4.5      2017-03-22 [1] CRAN (R 3.6.0)                                  
    viridis                                         0.5.1      2018-03-29 [1] CRAN (R 3.5.1)                                  
    viridisLite                                     0.3.0      2018-02-01 [1] CRAN (R 3.6.0)                                  
 V  webshot                                         0.5.1      2019-11-22 [1] CRAN (R 3.6.0)                                  
    WGCNA                                         * 1.68       2019-05-23 [1] CRAN (R 3.6.0)                                  
 P  withr                                           2.1.2      2018-03-15 [2] CRAN (R 3.6.0)                                  
 P  wordcloud                                       2.6        2018-08-24 [2] CRAN (R 3.6.0)                                  
 VP xfun                                            0.10       2019-11-12 [2] CRAN (R 3.6.0)                                  
 P  xlsx                                          * 0.6.1      2018-06-11 [2] CRAN (R 3.6.0)                                  
 P  xlsxjars                                        0.6.1      2014-08-22 [2] CRAN (R 3.6.0)                                  
 P  XML                                             3.98-1.20  2019-06-06 [2] CRAN (R 3.6.0)                                  
 P  xml2                                            1.2.2      2019-08-09 [2] CRAN (R 3.6.0)                                  
 P  xtable                                          1.8-4      2019-04-21 [2] CRAN (R 3.6.0)                                  
    XVector                                       * 0.24.0     2019-05-02 [1] Bioconductor                                    
    yaml                                            2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                                  
 P  zeallot                                         0.1.0      2018-01-28 [2] CRAN (R 3.6.0)                                  
    zlibbioc                                        1.30.0     2019-05-02 [1] Bioconductor                                    
 P  zoo                                             1.8-6      2019-05-28 [2] CRAN (R 3.6.0)                                  

[1] /users/home/bbose/R/x86_64-redhat-linux-gnu-library/3.5
[2] /users/home/bbose/R/x86_64-redhat-linux-gnu-library/3.6
[3] /usr/lib64/R/library
[4] /usr/share/R/library

 V ── Loaded and on-disk version mismatch.
 P ── Loaded and on-disk path mismatch.

Please help.

Thanks Bose

wvictor14 commented 4 years ago

**Error in read.metharray(basenames = commonFiles, extended = extended, :

[read.metharray] Trying to parse different IDAT files, of different size and type.**

Suggests you are trying to read in EPIC/450k data together. A quick look at GEO accession you can see that several idats are twice as large as others:

7MB 3.5MB

Try loading each set of 450k / 850k idats separately?

I would suggest, just arrange the files by size and then put them in separate folders, then read the folders in separately with the recursive = T option

boseb commented 4 years ago

Thanks!

Get Outlook for Androidhttps://aka.ms/ghei36

From: Victor Yuan notifications@github.com Sent: Friday, December 6, 2019 7:55:00 PM To: hansenlab/minfi minfi@noreply.github.com Cc: Bose, Banabithi banabithi.bose@marquette.edu; Author author@noreply.github.com Subject: Re: [hansenlab/minfi] Error in read.metharray(basenames = commonFiles, extended = extended, : [read.metharray] Trying to parse different IDAT files, of different size and type. (#195)

**Error in read.metharray(basenames = commonFiles, extended = extended, :

[read.metharray] Trying to parse different IDAT files, of different size and type.**

Suggests you are trying to read in EPIC/450k data together. A quick look at GEO accession you can see that several idats are twice as large as others:

7MBhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_geo_query_acc.cgi-3Facc-3DGSM3455824&d=DwMCaQ&c=S1d2Gs1Y1NQV8Lx35_Qi5FnTH2uYWyh_OhOS94IqYCo&r=Y9AYXRQMBdF6y5D9a5c7n_rNkgbQp1bOb8KjFhsj2gY&m=ZExpGdIM_gZHiZgl6UW4V_LQZmwmdaRGzmJ0_6o1Vvw&s=pFGnJ5IGGz3rWUb0cNe83ZCVrgQCZUZYeOjHRtJ2G9g&e= 3.5MBhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_geo_query_acc.cgi-3Facc-3DGSM3455766&d=DwMCaQ&c=S1d2Gs1Y1NQV8Lx35_Qi5FnTH2uYWyh_OhOS94IqYCo&r=Y9AYXRQMBdF6y5D9a5c7n_rNkgbQp1bOb8KjFhsj2gY&m=ZExpGdIM_gZHiZgl6UW4V_LQZmwmdaRGzmJ0_6o1Vvw&s=tzV_mw1LJMoIuWXibFBFPANEvr_B26Cds1wLHy9GR8Y&e=

Try loading each set of 450k / 850k idats separately?

I would suggest, just arrange the files by size and then put them in separate folders, then read the folders in separately with the recursive = T option

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hansenlab_minfi_issues_195-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAIAN2K27E7YQPP7KJBM2TQTQXL67JA5CNFSM4JXDWOLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGF27CA-23issuecomment-2D562802568&d=DwMCaQ&c=S1d2Gs1Y1NQV8Lx35_Qi5FnTH2uYWyh_OhOS94IqYCo&r=Y9AYXRQMBdF6y5D9a5c7n_rNkgbQp1bOb8KjFhsj2gY&m=ZExpGdIM_gZHiZgl6UW4V_LQZmwmdaRGzmJ0_6o1Vvw&s=nwAJl0Ow9eddBC1bAhnNOU0vYguNsxiwZdeWiHPVWhs&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIAN2K3WXTX3MA37BNIA733QXL67JANCNFSM4JXDWOLA&d=DwMCaQ&c=S1d2Gs1Y1NQV8Lx35_Qi5FnTH2uYWyh_OhOS94IqYCo&r=Y9AYXRQMBdF6y5D9a5c7n_rNkgbQp1bOb8KjFhsj2gY&m=ZExpGdIM_gZHiZgl6UW4V_LQZmwmdaRGzmJ0_6o1Vvw&s=kSF2fhE95t6XaIDt0IjYccrKV-NS9ZAaGHoWQNssF58&e=.