Package check result: OK Changes to worse in reverse depends: Package: compareGroups Check: examples New result: ERROR Running examples in ‘compareGroups-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compareSNPs > ### Title: Summarise genetic data by groups. > ### Aliases: compareSNPs print.compareSNPs > ### Keywords: misc > > ### ** Examples > > > require(compareGroups) > > # load example data > data(SNPs) > > # visualize first rows > head(SNPs) id casco sex blood.pre protein snp10001 snp10002 snp10003 snp10004 1 1 1 Female 13.7 75640.52 TT CC GG GG 2 2 1 Female 12.7 28688.22 TT AC GG GG 3 3 1 Female 12.9 17279.59 TT CC GG GG 4 4 1 Male 14.6 27253.99 CT CC GG GG 5 5 1 Female 13.4 38066.57 TT AC GG GG 6 6 1 Female 11.3 9872.46 TT CC GG GG snp10005 snp10006 snp10007 snp10008 snp10009 snp100010 snp100011 snp100012 1 GG AA CC CC AA TT GG GG 2 AG AA CC CC AG TT GG CG 3 GG AA CC CC AA TT CC GG 4 GG AA CC CC AA TT GG GG 5 GG AA CC CC AG TT GG GG 6 GG AA CC CC AA TT GG GG snp100013 snp100014 snp100015 snp100016 snp100017 snp100018 snp100019 1 AA AA GG GG TT TT CC 2 AA AC GG GG CT CT CG 3 AA CC GG GG TT TT CC 4 AA AC GG GG TT TT CG 5 AA AC GG GG CT CT CG 6 AA AA GG GG TT TT CC snp100020 snp100021 snp100022 snp100023 snp100024 snp100025 snp100026 1 GG GG AA TT TT CC GG 2 GG GG AA AT TT CC GG 3 GG GG AA TT TT CC GG 4 GG GG AA TT CT CC GG 5 GG GG AA AT TT CC GG 6 GG GG AA TT TT CC GG snp100027 snp100028 snp100029 snp100030 snp100031 snp100032 snp100033 1 CC CC GG AA TT AA AA 2 CG CT GG AA TT AG AG 3 CC CC GG AA TT AA AA 4 CC CT AG AA TT AG AG 5 CG CT GG AA TT AG AG 6 CC CC GG AA TT AA AA snp100034 snp100035 1 TT TT 2 TT TT 3 TT TT 4 CT TT 5 TT TT 6 TT > > # select casco and all SNPs > myDat <- SNPs[,c(2,6:40)] > > # QC of three SNPs by groups of cases and controls > res<-compareSNPs(casco ~ .-casco, myDat) Error in HWChisqStats(X, ...) : unused argument (verbose = FALSE) Calls: compareSNPs -> snpQC -> HWChisqMat Execution halted Package: compareGroups Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘compareGroups_vignette.Rmd’ using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-9'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-10'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-11'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-12'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-13'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-14'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-15'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-16'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-18'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-19'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-21'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-22'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-23'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-24'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-25'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-26'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-28'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-29'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-30'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-31'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-32'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-33'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-34'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-35'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-36'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-37'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-38'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-39'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-40'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-41'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-42'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-43'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-44'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-45'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-46'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-47'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-48'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-50'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-51'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-52'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-53'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-54'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-55'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-56'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-57'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-58'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-59'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-60'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-62'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-63'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-64'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-65'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-66'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-67'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-68'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-69'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-70'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-72'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-74'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-75'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-77'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-78'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-79'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-80'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-81'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-82'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-83'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-84'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-85'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-86'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-87'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-88'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-89'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-90'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-91'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-92'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-93'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-94'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-95'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-96'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-97'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-98'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-99'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-100'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-101'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-102'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Quitting from lines 1247-1249 [unnamed-chunk-102] (compareGroups_vignette.Rmd) Error: processing vignette 'compareGroups_vignette.Rmd' failed with diagnostics: unused argument (verbose = FALSE) --- failed re-building ‘compareGroups_vignette.Rmd’ SUMMARY: processing the following file failed: ‘compareGroups_vignette.Rmd’ Error: Vignette re-building failed. Execution halted