############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ToxicoGx.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ToxicoGx_2.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ToxicoGx.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ToxicoGx/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ToxicoGx' version '2.3.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'ToxicoGx' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': 'CoreGx:::updateSampleId' See the note in ?`:::` about the use of this operator. Missing object imported by a ':::' call: 'CoreGx:::updateTreamentId' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE computeLimmaDiffExpr,ToxicoSet: no visible global function definition for 'metadata<-' computeLimmaDiffExpr,ToxicoSet: no visible binding for global variable 'cell' Undefined global functions or variables: cell metadata<- * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 47 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'ToxicoGx-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ToxicoSet-accessors > ### Title: Accessing and modifying information in a 'CoreSet' > ### Aliases: ToxicoSet-accessors drugInfo treatmentInfo,ToxicoSet-method > ### treatmentInfo drugInfo<- treatmentInfo<-,ToxicoSet,data.frame-method > ### treatmentInfo<- drugNames treatmentNames,ToxicoSet-method > ### treatmentNames drugNames<- > ### treatmentNames<-,ToxicoSet,character-method treatmentNames<- > ### annotation,ToxicoSet-method annotation > ### annotation<-,ToxicoSet,list-method annotation<- > ### dateCreated,ToxicoSet-method dateCreated > ### dateCreated<-,ToxicoSet,character-method > ### dateCreated<-,ToxicoSet-method dateCreated<- name,ToxicoSet-method > ### name name<-,ToxicoSet-method name<-,ToxicoSet,character-method name<- > ### sampleInfo,ToxicoSet-method sampleInfo cellInfo,ToxicoSet-method > ### cellInfo sampleInfo<-,ToxicoSet,data.frame-method sampleInfo<- > ### cellInfo<-,ToxicoSet,data.frame-method cellInfo<- > ### sampleNames,ToxicoSet-method sampleName,ToxicoSet-method sampleNames > ### cellName,ToxicoSet-method cellNames > ### sampleNames<-,ToxicoSet,character-method > ### sampleNames<-,ToxicoSet,list-method sampleNames<- > ### cellNames<-,ToxicoSet,list-method cellNames<- > ### curation,ToxicoSet-method curation curation<-,ToxicoSet,list-method > ### curation<- datasetType,ToxicoSet-method datasetType > ### datasetType<-,ToxicoSet,character-method datasetType<- > ### molecularProfiles,ToxicoSet-method molecularProfiles > ### molecularProfiles<-,ToxicoSet,character,character,matrix-method > ### molecularProfiles<-,ToxicoSet,character,missing,matrix-method > ### molecularProfiles<-,ToxicoSet,missing,missing,list-method > ### molecularProfiles<-,ToxicoSet,missing,missing,MutliAssayExperiment-method > ### molecularProfiles<- featureInfo,ToxicoSet-method featureInfo > ### featureInfo<-,ToxicoSet,character,data.frame-method > ### featureInfo<-,ToxicoSet,character,DataFrame-method featureInfo<- > ### phenoInfo,ToxicoSet,character-method phenoInfo > ### phenoInfo<-,ToxicoSet,character,data.frame-method > ### phenoInfo<-,ToxicoSet,character,DataFrame-method phenoInfo<- > ### fNames,ToxicoSet,character-method fNames > ### fNames<-,ToxicoSet,character,character-method fNames<- > ### mDataNames,ToxicoSet-method mDataNames mDataNames<-,ToxicoSet-method > ### mDataNames<-,ToxicoSet,ANY-method mDataNames<- > ### molecularProfilesSlot,ToxicoSet-method > ### moleculerProfilesSlot,ToxicoSet-method molecularProfilesSlot > ### molecularProfilesSlot<-,ToxicoSet,list_OR_MAE-method > ### molecularProfilesSlot<-,ToxicoSet,list-method > ### molecularProfilesSlot<-ToxicoSet,MultiAssayExperiment-method > ### molecularProfilesSlot<- sensitivityInfo,ToxicoSet-method > ### sensitivityInfo,ToxicoSet,missing-method > ### sensitivityInfo,ToxicoSet,character-method > ### sensitivityInfo<-,ToxicoSet,data.frame-method > ### sensitivityInfo<-,ToxicoSet,missing,data.frame-method > ### sensitvityInfo<-,ToxicoSet,character,data.frame-method > ### sensitivityMeasures,ToxicoSet-method > ### sensitivityMeasures<-,ToxicoSet,character-method > ### sensitivityProfiles,ToxicoSet-method > ### sensitivityProfiles<-,ToxicoSet,data.frame-method > ### sensitivityRaw,ToxicoSet-method > ### sensitivityRaw<-,ToxicoSet,array-method > ### treatmentResponse,ToxicoSet-method treatmentResponse sensitivitySlot > ### treatmentResponse<-,ToxicoSet,list_OR_LongTable-method > ### treatmentResponse<- treamentResponse<-,ToxicoSet,list-method > ### treatmentResponse<-,ToxicoSet,LongTable-method sensitivitySlot<- > ### sensNumber,ToxicoSet-method sensNumber > ### sensNumber<-,ToxicoSet,matrix-method sensNumber<- > ### pertNumber,ToxicoSet-method pertNumber > ### pertNumber<-,ToxicoSet,array-method pertNumber<- > > ### ** Examples > > data(TGGATESsmall) > treatmentInfo(TGGATESsmall) treatmentid 1-Naphthyl isothiocyanate 1-Naphthyl isothiocyanate Phenylbutazone Phenylbutazone Rifampicin Rifampicin Indomethacin Indomethacin Chlorpromazine Chlorpromazine Isoniazid Isoniazid Acetaminophen Acetaminophen Clofibrate Clofibrate Carbon tetrachloride Carbon tetrachloride Phenobarbital Phenobarbital Methapyrilene Methapyrilene Ethionine Ethionine Carbamazepine Carbamazepine Cimetidine Cimetidine Fluphenazine Fluphenazine Pirinixic acid Pirinixic acid Aspirin Aspirin Gemfibrozil Gemfibrozil Labetalol Labetalol Hexachlorobenzene Hexachlorobenzene Amiodarone Amiodarone Allopurinol Allopurinol Benzbromarone Benzbromarone Nitrofurantoin Nitrofurantoin Diazepam Diazepam Griseofulvin Griseofulvin Sulfasalazine Sulfasalazine Bromobenzene Bromobenzene Cyclophosphamide Cyclophosphamide Omeprazole Omeprazole Allyl alcohol Allyl alcohol Valproic acid Valproic acid Diclofenac Diclofenac Propylthiouracil Propylthiouracil 2H-1-Benzopyran-2-one 2H-1-Benzopyran-2-one Haloperidol Haloperidol Tetracycline Tetracycline Flutamide Flutamide Glyburide Glyburide Azathioprine Azathioprine Perhexiline Perhexiline Phenytoin Phenytoin Doxepin Hydrochloride Doxepin Hydrochloride Thioridazine Thioridazine Methyltestosterone Methyltestosterone Lomustine Lomustine Thioacetamide Thioacetamide Xolegel Xolegel Ciprofloxacin Ciprofloxacin Pemoline Pemoline Chlormezanone Chlormezanone Metformin Metformin Tamoxifen Tamoxifen Ethinyl estradiol Ethinyl estradiol Methyldopa Methyldopa Methimazole Methimazole Monocrotaline Monocrotaline Retinol Retinol Quinidine Quinidine Tacrine Tacrine Moxisylyte Moxisylyte Iproniazid Iproniazid Chloramphenicol Chloramphenicol Nitrofurazone Nitrofurazone Trimipramine Trimipramine Amitriptyline Amitriptyline Hydroxyzine Hydroxyzine 2-(4-Isobutylphenyl)propanoic acid 2-(4-Isobutylphenyl)propanoic acid Naproxen Naproxen Furosemide Furosemide Fenofibrate Fenofibrate Chlorpropamide Chlorpropamide Nicotinic acid Nicotinic acid Erythromycin ethylsuccinate Erythromycin ethylsuccinate Ethambutol Ethambutol Mefenamic acid Mefenamic acid Pepcid Pepcid Ranitidine Ranitidine Tannic acid Tannic acid Captopril Captopril Caffeine Caffeine Papaverine Papaverine Enalapril Enalapril Theophylline Theophylline Sulindac Sulindac D-Penicillamine D-Penicillamine Disopyramide Disopyramide Mexiletine Mexiletine Acetazolamide Acetazolamide Disulfiram Disulfiram Colchicine Colchicine Nifedipine Nifedipine Diltiazem Diltiazem Chlorpheniramine Chlorpheniramine Tolbutamide Tolbutamide Acarbose Acarbose Simvastatin Simvastatin Meloxicam Meloxicam Chlormadinone Chlormadinone Benziodarone Benziodarone Ethionamide Ethionamide Nimesulide Nimesulide Ethanol Ethanol Bucetin Bucetin acetamidofluorene acetamidofluorene Ticlopidine Ticlopidine Tiopronin Tiopronin Promethazine Promethazine Sulpiride Sulpiride Dantrolene Dantrolene Clomipramine Clomipramine Terbinafine Terbinafine Lornoxicam Lornoxicam Danazol Danazol Etoposide Etoposide N-Phenylanthranilic acid N-Phenylanthranilic acid Ajmalin Ajmalin Phenacetin Phenacetin N-Nitrosodiethylamine N-Nitrosodiethylamine Alpidem Alpidem Venlafaxine Venlafaxine Clozapine Clozapine Buspirone Buspirone Nefazodone Nefazodone Triazolam Triazolam Trimethadione Trimethadione 2-Bromoethylamine 2-Bromoethylamine Doxorubicin Doxorubicin Cyclosporin A Cyclosporin A Cycloheximide Cycloheximide Phorone Phorone Bendazac Bendazac Buthionine sulfoximine Buthionine sulfoximine D-Galactosamine D-Galactosamine Diethyl maleate Diethyl maleate Rotenone Rotenone N,N'-Diphenylmethylenediamine N,N'-Diphenylmethylenediamine butylated hydroxyanisole butylated hydroxyanisole Fungizone Fungizone 2,4-Dinitrophenol 2,4-Dinitrophenol Fluoxetine hydrochloride Fluoxetine hydrochloride Dexamethasone Dexamethasone 2-Nitrofluorene 2-Nitrofluorene N-Methyl-N-nitrosourea N-Methyl-N-nitrosourea Acetamide Acetamide N-Nitrosomorpholine N-Nitrosomorpholine treatmentid_abbr treatmentid_no 1-Naphthyl isothiocyanate ANIT 00009 Phenylbutazone PhB 00011 Rifampicin RIF 00008 Indomethacin IM 00015 Chlorpromazine CPZ 00016 Isoniazid INAH 00002 Acetaminophen APAP 00001 Clofibrate CFB 00006 Carbon tetrachloride CCL4 00003 Phenobarbital PB 00004 Methapyrilene MP 00025 Ethionine ET 00013 Carbamazepine CBZ 00018 Cimetidine CIM 00035 Fluphenazine FP 00037 Pirinixic acid WY 00030 Aspirin ASA 00014 Gemfibrozil GFZ 00031 Labetalol LBT 00040 Hexachlorobenzene HCB 00022 Amiodarone AM 00033 Allopurinol APL 00028 Benzbromarone BBr 00021 Nitrofurantoin NFT 00020 Diazepam DZP 00023 Griseofulvin GF 00043 Sulfasalazine SS 00034 Bromobenzene BBZ 00032 Cyclophosphamide CPA 00024 Omeprazole OPZ 00012 Allyl alcohol AA 00010 Valproic acid VPA 00005 Diclofenac DFNa 00019 Propylthiouracil PTU 00029 2H-1-Benzopyran-2-one CMA 00027 Haloperidol HPL 00036 Tetracycline TC 00048 Flutamide FT 00044 Glyburide GBC 00042 Azathioprine AZP 00046 Perhexiline PH 00045 Phenytoin PHE 00026 Doxepin Hydrochloride ADP 00039 Thioridazine TRZ 00038 Methyltestosterone MTS 00041 Lomustine LS 00049 Thioacetamide TAA 00017 Xolegel KC 00047 Ciprofloxacin CPX 00050 Pemoline PML 00051 Chlormezanone CMN 00052 Metformin MFM 00053 Tamoxifen TMX 00054 Ethinyl estradiol EE 00055 Methyldopa MDP 00056 Methimazole MTZ 00057 Monocrotaline MCT 00058 Retinol VA 00059 Quinidine QND 00074 Tacrine TAC 00060 Moxisylyte MXS 00061 Iproniazid IPA 00062 Chloramphenicol CMP 00064 Nitrofurazone NFZ 00065 Trimipramine IMI 00069 Amitriptyline AMT 00070 Hydroxyzine HYZ 00071 2-(4-Isobutylphenyl)propanoic acid IBU 00072 Naproxen NPX 00073 Furosemide FUR 00078 Fenofibrate FFB 00079 Chlorpropamide CPP 00080 Nicotinic acid NIC 00081 Erythromycin ethylsuccinate EME 00082 Ethambutol EBU 00083 Mefenamic acid MEF 00084 Pepcid FAM 00085 Ranitidine RAN 00086 Tannic acid TAN 00093 Captopril CAP 00094 Caffeine CAF 00097 Papaverine PAP 00098 Enalapril ENA 00095 Theophylline TEO 00096 Sulindac SUL 00100 D-Penicillamine PEN 00099 Disopyramide DIS 00102 Mexiletine MEX 00103 Acetazolamide ACZ 00108 Disulfiram DSF 00109 Colchicine COL 00113 Nifedipine NIF 00091 Diltiazem DIL 00092 Chlorpheniramine CHL 00090 Tolbutamide TLB 00114 Acarbose ACA 00116 Simvastatin SST 00117 Meloxicam MLX 00124 Chlormadinone CLM 00126 Benziodarone BZD 00130 Ethionamide ETH 00135 Nimesulide NIM 00136 Ethanol ETN 00137 Bucetin BCT 00139 acetamidofluorene AAF 00144 Ticlopidine TCP 00146 Tiopronin TIO 00104 Promethazine PMZ 00110 Sulpiride SLP 00115 Dantrolene DTL 00119 Clomipramine CPM 00121 Terbinafine TBF 00123 Lornoxicam LNX 00125 Danazol DNZ 00127 Etoposide ETP 00131 N-Phenylanthranilic acid NPAA 00140 Ajmalin AJM 00118 Phenacetin PCT 00138 N-Nitrosodiethylamine DEN 00145 Alpidem ADM 00171 Venlafaxine VLF 00172 Clozapine CZP 00174 Buspirone BPR 00173 Nefazodone NZD 00175 Triazolam TZM 00120 Trimethadione TMD 00122 2-Bromoethylamine BEA 00134 Doxorubicin DOX 00149 Cyclosporin A CSA 00142 Cycloheximide CHX 00A01 Phorone PHO 00A03 Bendazac BDZ 00129 Buthionine sulfoximine BSO 00A04 D-Galactosamine GaN 00A06 Diethyl maleate DEM 00A05 Rotenone ROT 00152 N,N'-Diphenylmethylenediamine DAPM 00155 butylated hydroxyanisole BHA 00156 Fungizone AMB 00157 2,4-Dinitrophenol DNP 00154 Fluoxetine hydrochloride FLX 00158 Dexamethasone DEX 00153 2-Nitrofluorene 2NF 00160 N-Methyl-N-nitrosourea MNU 00164 Acetamide AAA 00169 N-Nitrosomorpholine NMOR 00163 > > treatmentInfo(TGGATESsmall) <- treatmentInfo(TGGATESsmall) > > treatmentNames(TGGATESsmall) [1] "1-Naphthyl isothiocyanate" "Phenylbutazone" [3] "Rifampicin" "Indomethacin" [5] "Chlorpromazine" "Isoniazid" [7] "Acetaminophen" "Clofibrate" [9] "Carbon tetrachloride" "Phenobarbital" [11] "Methapyrilene" "Ethionine" [13] "Carbamazepine" "Cimetidine" [15] "Fluphenazine" "Pirinixic acid" [17] "Aspirin" "Gemfibrozil" [19] "Labetalol" "Hexachlorobenzene" [21] "Amiodarone" "Allopurinol" [23] "Benzbromarone" "Nitrofurantoin" [25] "Diazepam" "Griseofulvin" [27] "Sulfasalazine" "Bromobenzene" [29] "Cyclophosphamide" "Omeprazole" [31] "Allyl alcohol" "Valproic acid" [33] "Diclofenac" "Propylthiouracil" [35] "2H-1-Benzopyran-2-one" "Haloperidol" [37] "Tetracycline" "Flutamide" [39] "Glyburide" "Azathioprine" [41] "Perhexiline" "Phenytoin" [43] "Doxepin Hydrochloride" "Thioridazine" [45] "Methyltestosterone" "Lomustine" [47] "Thioacetamide" "Xolegel" [49] "Ciprofloxacin" "Pemoline" [51] "Chlormezanone" "Metformin" [53] "Tamoxifen" "Ethinyl estradiol" [55] "Methyldopa" "Methimazole" [57] "Monocrotaline" "Retinol" [59] "Quinidine" "Tacrine" [61] "Moxisylyte" "Iproniazid" [63] "Chloramphenicol" "Nitrofurazone" [65] "Trimipramine" "Amitriptyline" [67] "Hydroxyzine" "2-(4-Isobutylphenyl)propanoic acid" [69] "Naproxen" "Furosemide" [71] "Fenofibrate" "Chlorpropamide" [73] "Nicotinic acid" "Erythromycin ethylsuccinate" [75] "Ethambutol" "Mefenamic acid" [77] "Pepcid" "Ranitidine" [79] "Tannic acid" "Captopril" [81] "Caffeine" "Papaverine" [83] "Enalapril" "Theophylline" [85] "Sulindac" "D-Penicillamine" [87] "Disopyramide" "Mexiletine" [89] "Acetazolamide" "Disulfiram" [91] "Colchicine" "Nifedipine" [93] "Diltiazem" "Chlorpheniramine" [95] "Tolbutamide" "Acarbose" [97] "Simvastatin" "Meloxicam" [99] "Chlormadinone" "Benziodarone" [101] "Ethionamide" "Nimesulide" [103] "Ethanol" "Bucetin" [105] "acetamidofluorene" "Ticlopidine" [107] "Tiopronin" "Promethazine" [109] "Sulpiride" "Dantrolene" [111] "Clomipramine" "Terbinafine" [113] "Lornoxicam" "Danazol" [115] "Etoposide" "N-Phenylanthranilic acid" [117] "Ajmalin" "Phenacetin" [119] "N-Nitrosodiethylamine" "Alpidem" [121] "Venlafaxine" "Clozapine" [123] "Buspirone" "Nefazodone" [125] "Triazolam" "Trimethadione" [127] "2-Bromoethylamine" "Doxorubicin" [129] "Cyclosporin A" "Cycloheximide" [131] "Phorone" "Bendazac" [133] "Buthionine sulfoximine" "D-Galactosamine" [135] "Diethyl maleate" "Rotenone" [137] "N,N'-Diphenylmethylenediamine" "butylated hydroxyanisole" [139] "Fungizone" "2,4-Dinitrophenol" [141] "Fluoxetine hydrochloride" "Dexamethasone" [143] "2-Nitrofluorene" "N-Methyl-N-nitrosourea" [145] "Acetamide" "N-Nitrosomorpholine" > > treatmentNames(TGGATESsmall) <- treatmentNames(TGGATESsmall) > > > ## @annotation > > annotation(TGGATESsmall) $name [1] "TGGATES Human LDH" $dateCreated [1] "Tue Mar 10 13:19:27 2020" $sessionInfo R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylibError in grepl(LAver, lapack, fixed = TRUE) : invalid 'pattern' argument Calls: -> print.sessionInfo -> grepl Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ToxicoGx.Rcheck/00check.log' for details.