* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘NGCHM’ ...
** package ‘NGCHM’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘NGCHM’
finding HTML links ... done
NGCHM-functions html
NGCHM-initialization html
NGCHM-package html
addition-methods html
cash-.shaidyRepo html
castAsInteger html
castListAsInteger html
chmAdd-method html
chmAddAxisType-method html
chmAddCSS-method html
chmAddColormap-method html
chmAddCovariate-method html
chmAddCovariateBar-method html
chmAddDataset-method html
chmAddDialog-method html
chmAddLayer-method html
chmAddMenuItem-method html
chmAddMetaData-method html
chmAddOverview-method html
chmAddPCA html
chmAddProperty-method html
chmAddReducedDim html
chmAddRelated-method html
chmAddRelatedGroup-method html
chmAddSpecificAxisTypeFunction-method html
chmAddTSNE html
chmAddTag-method html
chmAddTemplate-method html
chmAddToolboxR-method html
chmAddToolboxR2-method html
chmAddToolboxRC-method html
chmAddUMAP html
chmAddUWOT html
chmAxis html
chmAxisType html
chmBindFunction-method html
chmBrowse html
chmColOrder-method html
chmColorMap-set html
chmColorMap html
chmColors-set html
chmColors html
chmCovariate html
chmCovariateBar html
chmCreateCollection html
chmCreateManagedServer html
chmCreateServer html
chmCurrentCollection html
chmCurrentServer html
chmDefaultColOrder html
chmDefaultRowOrder html
chmDeployServer-method html
chmExportToFile-method html
chmExportToHTML-method html
chmExportToPDF-method html
chmFieldAccessFunction html
chmGetDataset-method html
chmGetDeployServerConfig html
chmGetFunction html
chmGetOverview html
chmGetProperty-method html
chmGetTypeInfo html
chmGetURL-method html
chmHasProperty-method html
chmInstall-method html
chmLabel-set html
chmLabel html
chmLayer-set html
chmLayer html
chmListFunctions html
chmListServers html
chmListTypes html
chmLoadCHM-method html
chmLoadShaidyCHM html
chmMake-method html
chmMakePrivate-method html
chmMakePublic-method html
chmManager html
chmName-method html
chmNew html
chmNewColorMap html
chmNewCovariate html
chmNewCovariateBar html
chmNewDataLayer html
chmNewDataset html
chmNewDialog html
chmNewFunction html
chmNewProperty html
chmNewServer html
chmOriginalColOrder html
chmOriginalRowOrder html
chmProperties html
chmProperty-set html
chmProperty html
chmRandomColOrder html
chmRandomRowOrder html
chmRegisterAxisFunction html
chmRegisterFunction html
chmRegisterGetMetadataFunction html
chmRegisterMatrixFunction html
chmRegisterToolboxFunction html
chmRegisterType html
chmRegisterTypeMapper html
chmRegisterTypeSplitter html
chmRowOrder-method html
chmServer html
chmSetCollection html
chmSetCredentials-method html
chmSetDeployServerConfig html
chmStringopFunction html
chmTreeGaps html
chmUninstall-method html
chmUrlBase-method html
chmWriteCustomJS html
getDimensions-method html
gitHashObject html
initLogging html
ngchm-class html
ngchmAddDatasetBlob html
ngchmAddMatrixToCollection html
ngchmAddObjectToCollection html
ngchmAxis-class html
ngchmAxisFunction-class html
ngchmAxisType-class html
ngchmBar-class html
ngchmCSS-class html
ngchmCollectionInCollection html
ngchmCollectionTree html
ngchmColormap-class html
ngchmCovariate-class html
ngchmCreateServerProtocol html
ngchmDataset-class html
ngchmDialog-class html
ngchmFindRepo html
ngchmGetDataFileShaid html
ngchmGetEnv html
ngchmGetHandleHTTR html
ngchmGetLabels html
ngchmGetLabelsStr html
ngchmGetProtoParam html
ngchmGetServerProtocol html
ngchmInitShaidyRepository html
ngchmJS-class html
ngchmLayer-class html
ngchmListServerProtocols html
ngchmLoadDatasetBlob html
ngchmMakeFormat.original html
ngchmMakeFormat.shaidy html
ngchmMatrixFunction-class html
ngchmMenuItem-class html
ngchmMetaData-class html
ngchmNewBar html
ngchmNewCollection html
ngchmOverview-class html
ngchmProperty-class html
ngchmProtoParamCheck html
ngchmPushSourceRepository html
ngchmPushSourceServer html
ngchmPushTempRepository html
ngchmRegisterServer html
ngchmRelated-class html
ngchmRelatedGroup-class html
ngchmRenderChm html
ngchmResponseJSON html
ngchmRowCenter html
ngchmSaveAsDatasetBlob html
ngchmSaveAsDendrogramBlob html
ngchmSaveChmAsBlob html
ngchmServer-class html
ngchmServerProtocol-class html
ngchmTemplate-class html
ngchmTileDataset html
ngchmTypeMapper-class html
ngchmUnregisterServer html
ngchmValueProp-class html
ngchmVersion2-class html
optDendrogram-class html
plot.ngchmVersion2 html
print.ngchm.type.info html
print.shaidyRepo html
shaid-class html
shaidyAddFileBlob html
shaidyBlobExists html
shaidyCopyBlob html
shaidyCreateProtoBlob html
shaidyFinalizeProtoBlob html
shaidyFindRepo html
shaidyGetComponents-method html
shaidyGetShaid-method html
shaidyHashProtoBlob html
shaidyInitRepository html
shaidyLoadProvenanceDB html
shaidyLoadProvidDB html
shaidyLoadRepository html
shaidyNewCache html
shaidyProvenance html
shaidyRepoAPI html
treeCuts-class html
verifyNumeric html
** building package indices
** testing if installed package can be loaded from temporary location
Warning in checkForNGCHMSupportFiles() :
CRITICAL WARNING: Package NGCHMSupportFiles is not installed. This package is required to create .ngchm and .html files. Please install and load NGCHMSupportFiles with commands:
install.packages('NGCHMSupportFiles', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))
library(NGCHMSupportFiles)
Warning in checkForNGCHMDemoData() :
NOTE: Package NGCHMDemoData is not installed. This package is used by the examples and website vignettes. Please install and load NGCHMDemoData with command:
install.packages('NGCHMDemoData', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))
library(NGCHMDemoData)
** testing if installed package can be loaded from final location
Warning in checkForNGCHMSupportFiles() :
CRITICAL WARNING: Package NGCHMSupportFiles is not installed. This package is required to create .ngchm and .html files. Please install and load NGCHMSupportFiles with commands:
install.packages('NGCHMSupportFiles', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))
library(NGCHMSupportFiles)
Warning in checkForNGCHMDemoData() :
NOTE: Package NGCHMDemoData is not installed. This package is used by the examples and website vignettes. Please install and load NGCHMDemoData with command:
install.packages('NGCHMDemoData', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))
library(NGCHMDemoData)
** testing if installed package keeps a record of temporary installation path
* creating tarball
Warning in utils::tar(filepath, curPkg, compression = "gzip", compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘NGCHM/help/chmAddSpecificAxisTypeFunction+2Cngchm+2Ccharacter+2Ccharacter+2Ccharacter+2Ccharacter-method.html’
Warning in utils::tar(filepath, curPkg, compression = "gzip", compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘NGCHM/help/chmAddSpecificAxisTypeFunction+2Cngchm+2Ccharacter+2Ccharacter+2Ccharacter+2CngchmJS-method.html’
packaged installation of ‘NGCHM’ as ‘NGCHM_1.0.2_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (NGCHM)