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BioC 3.4: BUILD report for NormqPCR on moscato1

This page was generated on 2016-09-21 03:43:33 -0700 (Wed, 21 Sep 2016).

Package 824/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.19.0
James Perkins
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/NormqPCR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded [ ERROR ] skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: NormqPCR
Version: 1.19.0
Command: chmod a+r NormqPCR -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data NormqPCR
StartedAt: 2016-09-19 23:02:17 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 23:02:31 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 13.9 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r NormqPCR -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data NormqPCR
###
##############################################################################
##############################################################################


* checking for file 'NormqPCR/DESCRIPTION' ... OK
* preparing 'NormqPCR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

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

Loading required package: affy
Loading required package: RColorBrewer
Loading required package: qpcR
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase

Attaching package: 'robustbase'

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

    rowMedians

Loading required package: Matrix
Warning in read.qPCR(qPCR.example.techReps) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

Warning in read.taqman(taqman.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

###############################################################

Step 1:

stability values M:

average stability M:	0.63628545246682

variable with lowest stability (largest M value):	ACTB

Pairwise variation, (9/10):	0.0764690052563778

###############################################################

Step 2:

stability values M:

average stability M:	0.582888329316757

variable with lowest stability (largest M value):	B2M

Pairwise variation, (8/9):	0.0776534266912183

###############################################################

Step 3:

stability values M:

average stability M:	0.530228279613623

variable with lowest stability (largest M value):	HMBS

Pairwise variation, (7/8):	0.0671119963410967

###############################################################

Step 4:

stability values M:

average stability M:	0.499943693933222

variable with lowest stability (largest M value):	TBP

Pairwise variation, (6/7):	0.0681320232188603

###############################################################

Step 5:

stability values M:

average stability M:	0.477377523800525

variable with lowest stability (largest M value):	SDHA

Pairwise variation, (5/6):	0.0806194432580746

###############################################################

Step 6:

stability values M:

average stability M:	0.437728198765878

variable with lowest stability (largest M value):	GAPD

Pairwise variation, (4/5):	0.0841653121631615

###############################################################

Step 7:

stability values M:

average stability M:	0.406770625156432

variable with lowest stability (largest M value):	HPRT1

Pairwise variation, (3/4):	0.097678269387021

###############################################################

Step 8:

stability values M:

average stability M:	0.371619241507029

variable with lowest stability (largest M value):	YWHAZ

Pairwise variation, (2/3):	0.113745049966055

###############################################################

Step 9:

stability values M:

average stability M:	0.349271187472188

Warning in .local(x, ...) :
  Argument 'group' is transformed to a factor vector.
Warning in .local(x, ...) :
  Argument 'group' is transformed to a factor vector.
Warning in .local(x, ...) :
  Argument 'group' is transformed to a factor vector.
###############################################################

Step 1:

stability values rho:

variable with highest stability (smallest rho value):	UBC

###############################################################

Step 2:

stability values rho:

variable with highest stability (smallest rho value):	GAPD

###############################################################

Step 3:

stability values rho:

variable with highest stability (smallest rho value):	TPT1

###############################################################

Step 4:

stability values rho:

variable with highest stability (smallest rho value):	UBB

###############################################################

Step 5:

stability values rho:

variable with highest stability (smallest rho value):	RPS13

###############################################################

Step 6:

stability values rho:

variable with highest stability (smallest rho value):	ACTB

###############################################################

Step 7:

stability values rho:

variable with highest stability (smallest rho value):	SUI1

###############################################################

Step 8:

stability values rho:

variable with highest stability (smallest rho value):	NACA

###############################################################

Step 9:

stability values rho:

variable with highest stability (smallest rho value):	CFL1

###############################################################

Step 10:

stability values rho:

variable with highest stability (smallest rho value):	FLJ20030

###############################################################

Step 11:

stability values rho:

variable with highest stability (smallest rho value):	TUBA6

###############################################################

Step 12:

stability values rho:

variable with highest stability (smallest rho value):	CLTC

Warning in .local(x, ...) :
  Argument 'group' is transformed to a factor vector.
Warning in read.taqman(taqman.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

Warning in read.taqman(taqman.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in read.taqman(taqman.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in read.taqman(taqman.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Control
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in .local(qPCRBatch, ...) : No Detector for Case
Warning in read.qPCR(qPCR.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.


Error: processing vignette 'NormqPCR.Rnw' failed with diagnostics:
 chunk 30 (label = ComputeNRQs3) 
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
Execution halted