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 | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data NormqPCR
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* checking for file ‘NormqPCR/DESCRIPTION’ ... OK
* preparing ‘NormqPCR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... 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
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
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.
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Step 1:
stability values M:
average stability M: 0.63628545246682
variable with lowest stability (largest M value): ACTB
Pairwise variation, (9/10): 0.0764690052563778
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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
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Step 4:
stability values M:
average stability M: 0.499943693933222
variable with lowest stability (largest M value): TBP
Pairwise variation, (6/7): 0.0681320232188603
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Step 5:
stability values M:
average stability M: 0.477377523800525
variable with lowest stability (largest M value): SDHA
Pairwise variation, (5/6): 0.0806194432580746
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Step 6:
stability values M:
average stability M: 0.437728198765878
variable with lowest stability (largest M value): GAPD
Pairwise variation, (4/5): 0.0841653121631615
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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
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Step 2:
stability values rho:
variable with highest stability (smallest rho value): GAPD
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Step 3:
stability values rho:
variable with highest stability (smallest rho value): TPT1
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Step 4:
stability values rho:
variable with highest stability (smallest rho value): UBB
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Step 5:
stability values rho:
variable with highest stability (smallest rho value): RPS13
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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
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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
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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