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