Back to Multiple platform build/check report for BioC 3.7
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

BUILD report for rexposome on malbec2

This page was generated on 2018-10-17 08:30:31 -0400 (Wed, 17 Oct 2018).

Package 1225/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.2.0
Carles Hernandez-Ferrer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/rexposome
Branch: RELEASE_3_7
Last Commit: 11419ba
Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: rexposome
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rexposome
StartedAt: 2018-10-15 21:42:00 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 21:43:39 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 99.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rexposome
###
##############################################################################
##############################################################################


* checking for file ‘rexposome/DESCRIPTION’ ... OK
* preparing ‘rexposome’:
* 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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, 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")'.


Attaching package: 'rexposome'

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

    plotPCA

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 76 rows containing non-finite values (stat_bin).
Warning: Removed 76 rows containing non-finite values (stat_density).
Warning in log(dta$value) : NaNs produced
Warning in sqrt(dta$value) : NaNs produced
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 338 rows containing non-finite values (stat_bin).
Warning: Removed 338 rows containing non-finite values (stat_density).
Warning in standardize(exp, method = "normal") :
  Given categorical exposures.
Warning in standardize(exp, method = "normal") :
  Categorical exposures will not be standardized.
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Using Exposure as id variables
Using Dim as id variables
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜AbsPM25+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜As+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE100+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE138+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE153+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE154+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE17+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE183+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE190+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE209+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE28+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE47+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE66+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE71+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE85+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BDE99+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BPA+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜BTHM+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Benzene+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜CHCl3+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Cd+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Co+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Conn+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Cotinine+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Cs+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Cu+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜DDE+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜DDT+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Dens+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜ETS+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜G_pesticides+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Gas+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Green+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜HCB+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜H_pesticides+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Hg+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MBzP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MEHHP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MEHP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MEOHP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MEP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MiBP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜MnBP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Mo+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜NO+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜NO2+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜NOx+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Ni+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Noise_d+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Noise_n+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PCB118+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PCB138+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PCB153+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PCB180+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PFHxS+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PFNA+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PFOA+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PFOS+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10Cu+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10Fe+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10K+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10Ni+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10S+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10SI+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10V+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM10Zn+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25CU+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25FE+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25K+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25Ni+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25S+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25Sl+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25V+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PM25Zn+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜PMcoarse+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Pb+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Sb+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Se+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜THM+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Temp+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Tl+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜X2cxMMHP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜X5cxMEPP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜X7OHMMeOP+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜Zn+sex + age' was reduced from 109 to 107
Warning in exwas(exp, formula = blood_pre ˜ sex + age, family = "gaussian") :
  Data from 'blood_pre˜bHCH+sex + age' was reduced from 109 to 107
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in chisq.test(...) : Chi-squared approximation may be incorrect
Warning in mexwas(exp_std, phenotype = "blood_pre", family = "gaussian") :
  Given phenotype (blood_pre) has NA values. 2 samples will be discarded.
Warning in mexwas(exp_std, phenotype = "blood_pre", family = "gaussian") :
  Categorical exposures will be droped and not used in the analysis.
Warning in mexwas(exp_std, phenotype = "wheezing", family = "binomial") :
  Categorical exposures will be droped and not used in the analysis.
Loading required package: lattice

Attaching package: 'mice'

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

    cbind, rbind

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

    cbind, rbind

Quitting from lines 229-231 (mutiple_imputation_data_analysis.Rmd) 
Error: processing vignette 'mutiple_imputation_data_analysis.Rmd' failed with diagnostics:
'names' attribute [4] must be the same length as the vector [0]
Execution halted