| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:13 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 PhenStat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhenStat.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1487/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhenStat 2.37.0 (landing page) Hamed Haselimashhadi
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: PhenStat |
| Version: 2.37.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data PhenStat |
| StartedAt: 2023-05-26 00:33:38 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 00:34:15 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 37.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data PhenStat
###
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* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* preparing ‘PhenStat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘PhenStat.Rnw’ using Sweave
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.
Information:
Dataset's 'Genotype' column has following values: '+/+', 'Sparc/Sparc'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.
Information:
Dataset's 'Genotype' column has following values: '+/+', 'Mysm1/+'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.
Information:
Dataset's 'Genotype' column has following values: '+/+', 'Mysm1/+'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.
Warning:
Dataset has been cleaned by filtering out records with genotype value other than test genotype 'Arid4a/Arid4a' or reference genotype '+/+'.
Information:
Dataset's 'Genotype' column has following values: '+/+', 'Arid4a/Arid4a'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Information:
Dependent variable: 'Bone.Area'.
Information:
Perform all MM framework stages: startModel and finalModel.
Information:
Method: Mixed Model framework.
Information:
Equation: 'withoutWeight'.
Information:
Calculated values for model effects are: keep_Batch=TRUE, keep_EqualVariance=TRUE, keep_Weight=FALSE, keep_Sex=TRUE, keep_Interaction=FALSE.
Information:
Dependent variable: 'Bone.Area'.
Information:
Method: Mixed Model framework.
Information:
Equation: 'withoutWeight'.
Information:
Calculated values for model effects are: keep_Batch=TRUE, keep_EqualVariance=TRUE, keep_Weight=FALSE, keep_Sex=TRUE, keep_Interaction=FALSE.
Information:
Dependent variable: 'Bone.Area'.
Information:
Method: Mixed Model framework.
Information:
Equation: 'withoutWeight'.
Information:
Calculated values for model effects are: keep_Batch=TRUE, keep_EqualVariance=TRUE, keep_Weight=FALSE, keep_Sex=TRUE, keep_Interaction=FALSE.
Information:
User's values for model effects are: keep_Batch=TRUE, keep_EqualVariance=TRUE, keep_Weight=FALSE, keep_Sex=TRUE, keep_Interaction=TRUE.
Warning:
Calculated values differ from user defined values for model effects.
Test for dependent variable:
*** Bone.Area ***
Method:
*** Mixed Model framework ***
----------------------------------------------------------------------------
Model Output
----------------------------------------------------------------------------
Final fitted model: Bone.Area ~ Sex + Genotype:Sex
Was batch significant? TRUE
Was variance equal? TRUE
Genotype p-value: 1.161054e-02
Genotype by male effect: -2.436094e-01 +/- 2.506629e-01
Genotype by female effect: -7.453442e-01 +/- 2.640284e-01
Was there evidence of sexual dimorphism? yes (p-value 1.740753e-01)
Genotype percentage change Female: -7.77%
Genotype percentage change Male: -2.54%
----------------------------------------------------------------------------
Classification Tag
----------------------------------------------------------------------------
With phenotype threshold value 0.01 - no significant change
----------------------------------------------------------------------------
Model Output Summary
----------------------------------------------------------------------------
Information:
Dataset's 'Genotype' column has following values: 'WT', 'het'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Data points containing 'Cholesterol' by batch levels:
| ----------- | ----------- | ----------- | ----------- | ----------- |
| | WT | WT | het | het |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| Batch | Female | Male | Female | Male |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2012-04-08 | 7 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-03-11 | 7 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-05-13 | 7 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-05-21 | 7 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-05-27 | 7 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-06-03 | 4 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-07-08 | 0 | 2 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-07-15 | 5 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-07-22 | 3 | 2 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-07-29 | 7 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-08-05 | 2 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-09-02 | 7 | 4 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-09-09 | 4 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-09-16 | 2 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-10-14 | 7 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-10-21 | 7 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-10-28 | 2 | 4 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-11-04 | 3 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-11-11 | 5 | 4 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-11-18 | 3 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-11-25 | 4 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2013-12-09 | 6 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-01-07 | 5 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-01-08 | 5 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-01-13 | 4 | 2 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-01-14 | 5 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-01-20 | 2 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-01-27 | 2 | 9 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-02-03 | 0 | 1 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| 2014-02-17 | 6 | 4 | 3 | 4 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| 2014-02-18 | 0 | 3 | 2 | 3 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-03 | 6 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-04 | 2 | 2 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-10 | 2 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-17 | 4 | 5 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-18 | 4 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-24 | 4 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-03-31 | 3 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-04-07 | 2 | 4 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| 2014-04-14 | 0 | 4 | 4 | 3 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-04-28 | 4 | 6 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-05-05 | 2 | 3 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-05-12 | 9 | 9 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-05-20 | 3 | 1 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-05-26 | 3 | 4 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-06-10 | 1 | 7 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-06-16 | 8 | 8 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
| * 2014-06-23 | 3 | 4 | 0 | 0 |
| ----------- | ----------- | ----------- | ----------- | ----------- |
* - removed record(s)
Number of batch levels left: 3
Records removed (reference genotype): 92% [exact : 91.8552036199095%]
Records removed (test genotype): 0% [exact : 0%]
Information:
Dependent variable: 'Cholesterol'.
Information:
Perform all TF framework stages: startTFModel and finalTFModel.
Information:
Method: Time as Fixed Effect framework.
Information:
Equation: 'withWeight'.
Information:
Calculated values for model effects are: keepBatch=TRUE, keepEqualVariance=FALSE, keepWeight=TRUE, keepSex=FALSE, keepInteraction=TRUE.
Test for dependent variable:
*** Cholesterol ***
Method:
*** Time as Fixed Effect framework ***
----------------------------------------------------------------------------
Model Output
----------------------------------------------------------------------------
Final fitted model: Cholesterol ~ Sex + Genotype:Sex + Weight + Batch
Was batch significant? TRUE
Was variance equal? FALSE
Genotype p-value: 4.899369e-05
Genotype by male effect: -5.124292e-01 +/- 1.108359e-01
Genotype by female effect: 2.717280e-02 +/- 1.223334e-01
Was there evidence of sexual dimorphism? yes (p-value 2.330644e-03)
Genotype percentage change Female: 1.25%
Genotype percentage change Male: -23.52%
----------------------------------------------------------------------------
Classification Tag
----------------------------------------------------------------------------
With phenotype threshold value 0.01 - males only
----------------------------------------------------------------------------
Model Output Summary
----------------------------------------------------------------------------
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.
Information:
Dataset's 'Genotype' column has following values: '+/+', 'Sparc/Sparc'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Information:
Dependent variable: 'Lean.Mass'.
Information:
Method: Reference Ranges Plus framework with filtered dataset.
Test for dependent variable:
*** Lean.Mass ***
Method:
*** Reference Ranges Plus framework ***
----------------------------------------------------------------------------
Classification Tag
----------------------------------------------------------------------------
Not significant
----------------------------------------------------------------------------
Thresholds
----------------------------------------------------------------------------
----------------------------------------------------------------------------
Count Matrices
----------------------------------------------------------------------------
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.
Warning:
Dataset has been cleaned by filtering out records with genotype value other than test genotype 'Aff3/Aff3' or reference genotype '+/+'.
Warning:
Dataset's 'Weight' column is missed.
You can define 'dataset.colname.weight' argument to specify column for the weight effect modeling.
Information:
Dataset's 'Genotype' column has following values: '+/+', 'Aff3/Aff3'
Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'
Warning:
Weight column is not present in the database.
Information:
Dependent variable: 'Thoracic.Processes'.
Information:
Method: Fisher Exact Test framework with filtered dataset.
Test for dependent variable:
*** Thoracic.Processes ***
Method:
*** Fisher Exact Test framework ***
----------------------------------------------------------------------------
Model Output ('*' highlights results with p-values less than threshold 0.01)
----------------------------------------------------------------------------
----------------------------------------------------------------------------
Classification Tag
----------------------------------------------------------------------------
With phenotype threshold value 0.01 - significant in males, females and in combined dataset
----------------------------------------------------------------------------
Count Matrices
----------------------------------------------------------------------------
Test for dependent variable:
*** Lean.Mass ***
Method:
*** Mixed Model framework ***
----------------------------------------------------------------------------
Model Output
----------------------------------------------------------------------------
Final fitted model: Lean.Mass ~ Genotype + Sex + Weight
Was batch significant? TRUE
Was variance equal? FALSE
Genotype p-value: 3.715089e-01
Genotype effect: -2.914359e-01 +/- 3.304800e-01
Was there evidence of sexual dimorphism? no (p-value 1.022353e-01)
Genotype percentage change Female: -1.44%
Genotype percentage change Male: -1.44%
----------------------------------------------------------------------------
Classification Tag
----------------------------------------------------------------------------
With phenotype threshold value 0.01 - no significant change
----------------------------------------------------------------------------
Model Output Summary
----------------------------------------------------------------------------
Test for dependent variable:
*** Thoracic.Processes ***
Method:
*** Fisher Exact Test framework ***
----------------------------------------------------------------------------
Model Output ('*' highlights results with p-values less than threshold 0.01)
----------------------------------------------------------------------------
----------------------------------------------------------------------------
Classification Tag
----------------------------------------------------------------------------
With phenotype threshold value 0.01 - significant in males, females and in combined dataset
----------------------------------------------------------------------------
Count Matrices
----------------------------------------------------------------------------
Error: processing vignette 'PhenStat.Rnw' failed with diagnostics:
unable to run pdflatex on 'PhenStat.tex'
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.8 \usepackage
{url}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘PhenStat.Rnw’
SUMMARY: processing the following file failed:
‘PhenStat.Rnw’
Error: Vignette re-building failed.
Execution halted