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This page was generated on 2023-02-08 01:15:04 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
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To the developers/maintainers of the GCSscore package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GCSscore.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. |
| Package 731/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GCSscore 1.13.0 (landing page) Guy M. Harris
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: GCSscore |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GCSscore |
| StartedAt: 2023-02-06 08:27:14 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 08:31:56 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 281.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GCSscore
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* checking for file ‘GCSscore/DESCRIPTION’ ... OK
* preparing ‘GCSscore’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GCSscore.Rnw’ using Sweave
GCSscore supports the selected chip-type: Clariom_S_Mouse
Bioconductor platform design (.pd) package already installed for: Clariom_S_Mouse
GCS-score analysis initiated for chip-type: Clariom_S_Mouse
The latest verison (0.0.5) of the GCS-score 'probeFile' package already installed for chip-type: Clariom_S_Mouse
typeFilter set to (0) by default for best .CEL file scaling and normalization statistics
all probe_id types (including control probe_ids and bgp probe_ids) will be for GCS-score calculation.
it is generally recommended to leave the typeFilter option set to (0)
** Checking if Bioconductor annotation (.db) packages are installed chip-type: Clariom_S_Mouse **
Annotation package (clariomsmousetranscriptcluster.db) already installed for chip-type: Clariom_S_Mouse
The latest verison (0.0.5) of the transcript-level netaffx-based annotation package already installed for chip-type: Clariom_S_Mouse
*NOTE: 'method' is automatically set to (1) (transcript_cluster_id-level) for all ClariomS arrays
*Performing gene-level analysis (by 'transcript_cluster_id')
loading probeFile from package: clariomsmouse.probeFile
loading annotations from package: clariomsmouse.TC.netaffx.annot
cannot disable removal of outliers and masked probes for non 3'-IVT chip types
*********************************
**** begin GCS-score analysis ***
*********************************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
** GCS-score analysis complete **
*********************************
GCSscore supports the selected chip-type: Clariom_S_Mouse
Bioconductor platform design (.pd) package already installed for: Clariom_S_Mouse
GCS-score analysis initiated for chip-type: Clariom_S_Mouse
The latest verison (0.0.5) of the GCS-score 'probeFile' package already installed for chip-type: Clariom_S_Mouse
typeFilter set to (0) by default for best .CEL file scaling and normalization statistics
all probe_id types (including control probe_ids and bgp probe_ids) will be for GCS-score calculation.
it is generally recommended to leave the typeFilter option set to (0)
** Checking if Bioconductor annotation (.db) packages are installed chip-type: Clariom_S_Mouse **
Annotation package (clariomsmousetranscriptcluster.db) already installed for chip-type: Clariom_S_Mouse
The latest verison (0.0.5) of the transcript-level netaffx-based annotation package already installed for chip-type: Clariom_S_Mouse
*NOTE: 'method' is automatically set to (1) (transcript_cluster_id-level) for all ClariomS arrays
*Performing gene-level analysis (by 'transcript_cluster_id')
loading probeFile from package: clariomsmouse.probeFile
loading annotations from package: clariomsmouse.TC.netaffx.annot
cannot disable removal of outliers and masked probes for non 3'-IVT chip types
*********************************
**** begin GCS-score analysis ***
*********************************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
*custom run name (column name) for BATCH job:
example01
**** run completed ****
***********************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
*custom run name (column name) for BATCH job:
example02
**** run completed ****
***********************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
*custom run name (column name) for BATCH job:
example03
**** run completed ****
***********************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
*custom run name (column name) for BATCH job:
example04
**** run completed ****
***********************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
*custom run name (column name) for BATCH job:
example05
**** run completed ****
***********************
reading .CEL files
calculating scaling factors (SF1 & SF2)
calculating rawQ and SDT values
calculating and normalizing GCS-score results
*custom run name (column name) for BATCH job:
example06
**** run completed ****
***********************
** GCS-score analysis complete **
*********************************
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2769nnn/GSM2769665/suppl//GSM2769665_01_N-1_Naive_08-23-16_S2_Clariom_S_Mouse_.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 1018304 bytes (994 KB)
==================================================
downloaded 994 KB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2769nnn/GSM2769666/suppl//GSM2769666_02_NM-2_repl_Naive_08-23-16_S2_Clariom_S_Mouse_.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 1032015 bytes (1007 KB)
==================================================
downloaded 1007 KB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2769nnn/GSM2769667/suppl//GSM2769667_03_NF-3_repl_Naive_08-23-16_S2_Clariom_S_Mouse_.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 993300 bytes (970 KB)
==================
downloaded 368 KB
Error: processing vignette 'GCSscore.Rnw' failed with diagnostics:
chunk 10
Error in GEOquery::getGEOSuppFiles(GEO = x, makeDirectory = FALSE, baseDir = dir.geo, :
Failed to download /tmp/RtmpcUGZqU/GSE103380/GSM2769667_03_NF-3_repl_Naive_08-23-16_S2_Clariom_S_Mouse_.CEL.gz!
--- failed re-building ‘GCSscore.Rnw’
SUMMARY: processing the following file failed:
‘GCSscore.Rnw’
Error: Vignette re-building failed.
Execution halted