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This page was generated on 2022-06-24 12:07:59 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for profileplyr on merida1


To the developers/maintainers of the profileplyr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/profileplyr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1501/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
profileplyr 1.12.0  (landing page)
Tom Carroll , Doug Barrows
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/profileplyr
git_branch: RELEASE_3_15
git_last_commit: cabfef2
git_last_commit_date: 2022-04-26 11:54:38 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: profileplyr
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data profileplyr
StartedAt: 2022-06-23 20:39:40 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 20:56:51 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 1031.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data profileplyr
###
##############################################################################
##############################################################################


* checking for file ‘profileplyr/DESCRIPTION’ ... OK
* preparing ‘profileplyr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘profileplyr.Rmd’ using rmarkdown
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians





Attaching package: 'profileplyr'

The following object is masked from 'package:S4Vectors':

    params

Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Making ChIPprofile object from signal files.
Reading Bam header information.....Done
Filtering regions which extend outside of genome boundaries.....Done
Filtered 0 of 3 regions
Splitting regions by Watson and Crick strand....Done
..Done
Found 3 Watson strand regions
Found 0 Crick strand regions
Extending regions.....done
Reading tags from /private/tmp/RtmplN8TWu/Rinst1253147eeee44/profileplyr/extdata/Sorted_Hindbrain_day_12_1_filtered.bam..Done.
Read in 7763 reads
Extending reads to fragmentlength of 150..done
Calculating coverage....done
Making windows.
Windowing positive 5' flanking 
Windowing positive regions 
Windowing positive 3' flank 
..done

Calculating bin scores for regions.
Processing per contig
contig: 1
Processing inner region windows in chr4
..done
Processing flanking windows in chr4
contig: 2
Processing inner region windows in chr13
..done
Processing flanking windows in chr13
contig: 3
Processing inner region windows in chr15
..done
Processing flanking windows in chr15
Reading Bam header information.....Done
Filtering regions which extend outside of genome boundaries.....Done
Filtered 0 of 3 regions
Splitting regions by Watson and Crick strand....Done
..Done
Found 3 Watson strand regions
Found 0 Crick strand regions
Extending regions.....done
Reading tags from /private/tmp/RtmplN8TWu/Rinst1253147eeee44/profileplyr/extdata/Sorted_Liver_day_12_1_filtered.bam..Done.
Read in 0 reads
Extending reads to fragmentlength of 150..done
Calculating coverage....done
Making windows.
Windowing positive 5' flanking 
Windowing positive regions 
Windowing positive 3' flank 
..done

Calculating bin scores for regions.
Processing per contig
contig: 1
Processing inner region windows in chr4
..done
Processing flanking windows in chr4
contig: 2
Processing inner region windows in chr13
..done
Processing flanking windows in chr13
contig: 3
Processing inner region windows in chr15
..done
Processing flanking windows in chr15
Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
No 'kmeans_k' or 'cutree_rows' arguments specified. profileplyr object will be returned new column with hierarchical order from hclust
K means clustering used.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
K means clustering used.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
Hierarchical clustering used. It is advised to avoid this option with large matrices as the clustering can take a long time. Kmeans is more suitable for large matrices.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.

Attaching package: 'magrittr'

The following object is masked from 'package:GenomicRanges':

    subtract

Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
K means clustering used.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
Loading required package: org.Mm.eg.db
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (1st try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (2nd try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (3th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (4th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (5th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (6th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (7th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (8th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (9th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
failed with the request, try after 0 min (10th try)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to great.stanford.edu port 80: Operation timed out
Quitting from lines 446-450 (profileplyr.Rmd) 
Error: processing vignette 'profileplyr.Rmd' failed with diagnostics:
max try: 10 reached. Stop with error.

--- failed re-building ‘profileplyr.Rmd’

SUMMARY: processing the following file failed:
  ‘profileplyr.Rmd’

Error: Vignette re-building failed.
Execution halted