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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BiocSet
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* checking for file ‘BiocSet/DESCRIPTION’ ... OK
* preparing ‘BiocSet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BiocSet.Rmd’ using rmarkdown
Quitting from BiocSet.Rmd:260-271 [file_cache]
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<error/rlang_error>
Error in `if (.self$lastField == "REFERENCE") ...`:
! missing value where TRUE/FALSE needed
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Backtrace:
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1. └─BiocSet::kegg_sets("hsa")
2. └─base::lapply(...)
3. └─BiocSet (local) FUN(X[[i]], ...)
4. └─KEGGREST::keggGet(x)
5. └─KEGGREST:::.getUrl(url, .flatFileParser)
6. ├─base::do.call(parser, list(content, ...))
7. └─KEGGREST (local) `<fn>`("ENTRY hsa01100 Global Pathway\nNAME Metabolic pathways - Homo sapiens (human)\nPATHWAY_MAP hsa01100 Metabolic pathways\nMODULE hsa_M00001 Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:hsa01100]\n hsa_M00002 Glycolysis, core module involving three-carbon compounds [PATH:hsa01100]\n hsa_M00003 Gluconeogenesis, oxaloacetate => fructose-6P [PATH:hsa01100]\n hsa_M00004 Pentose phosphate pathway (Pentose phosphate cycle) [PATH:hsa01100]\n hsa_M00005 PRPP biosynthesis, ribose 5P => PRPP [PATH:hsa01100]\n hsa_M00006 Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:hsa01100]\n hsa_M00007 Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:hsa01100]\n hsa_M00009 Citrate cycle (TCA cycle, Krebs cycle) [PATH:hsa01100]\n hsa_M00010 Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:hsa01100]\n hsa_M00011 Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:hsa01100]\n hsa_M00014 Glucuronate pathway (uronate pathway) [PATH:hsa01100]\n hsa_M00015 Proline biosynthesis, glutamate => proline [PATH:hsa01100]\n hsa_M00020 Serine biosynthesis, glycerate-3P => serine [PATH:hsa01100]\n hsa_M00027 GABA (gamma-Aminobutyrate) shunt [PATH:hsa01100]\n hsa_M00029 Urea cycle [PATH:hsa01100]\n hsa_M00032 Lysine degradation, lysine => saccharopine => acetoacetyl-CoA [PATH:hsa01100]\n hsa_M00034 Methionine salvage pathway [PATH:hsa01100]\n hsa_M00035 Methionine degradation [PATH:hsa01100]\n hsa_M00036 Leucine degradation, leucine => acetoacetate + acetyl-CoA [PATH:hsa01100]\n hsa_M00037 Melatonin biosynthesis, animals, tryptophan => serotonin => melatonin [PATH:hsa01100]\n hsa_M00038 Tryptophan metabolism, tryptophan => kynurenine => 2-aminomuconate [PATH:hsa01100]\n hsa_M00042 Catecholamine biosynthesis, tyrosine => dopamine => noradrenaline => adrenaline [PATH:hsa01100]\n hsa_M00043 Thyroid hormone biosynthesis, tyrosine => triiodothyronine/thyroxine [PATH:hsa01100]\n hsa_M00044 Tyrosine degradation, tyrosine => homogentisate [PATH:hsa01100]\n hsa_M00045 Histidine degradation, histidine => N-formiminoglutamate => glutamate [PATH:hsa01100]\n hsa_M00046 Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate [PATH:hsa01100]\n hsa_M00047 Creatine pathway [PATH:hsa01100]\n hsa_M00048 De novo purine biosynthesis, PRPP + glutamine => IMP [PATH:hsa01100]\n hsa_M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:hsa01100]\n hsa_M00050 Guanine ribonucleotide biosynthesis, IMP => GDP,GTP [PATH:hsa01100]\n hsa_M00051 De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMP [PATH:hsa01100]\n hsa_M00052 Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:hsa01100]\n hsa_M00053 Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP [PATH:hsa01100]\n hsa_M00056 O-glycan biosynthesis, mucin type core [PATH:hsa01100]\n hsa_M00057 Glycosaminoglycan biosynthesis, linkage tetrasaccharide [PATH:hsa01100]\n hsa_M00058 Glycosaminoglycan biosynthesis, chondroitin sulfate backbone [PATH:hsa01100]\n hsa_M00059 Glycosaminoglycan biosynthesis, heparan sulfate backbone [PATH:hsa01100]\n hsa_M00065 GPI-anchor biosynthesis, core oligosaccharide [PATH:hsa01100]\n hsa_M00066 Lactosylceramide biosynthesis [PATH:hsa01100]\n hsa_M00067 Sulfoglycolipids biosynthesis, ceramide/1-alkyl-2-acylglycerol => sulfatide/seminolipid [PATH:hsa01100]\n hsa_M00068 Glycosphingolipid biosynthesis, globo-series, LacCer => Gb4Cer [PATH:hsa01100]\n hsa_M00069 Glycosphingolipid biosynthesis, ganglio series, LacCer => GT3 [PATH:hsa01100]\n hsa_M00070 Glycosphingolipid biosynthesis, lacto-series, LacCer => Lc4Cer [PATH:hsa01100]\n hsa_M00071 Glycosphingolipid biosynthesis, neolacto-series, LacCer => nLc4Cer [PATH:hsa01100]\n hsa_M00073 N-glycan precursor trimming [PATH:hsa01100]\n hsa_M00075 N-glycan biosynthesis, complex type [PATH:hsa01100]\n hsa_M00076 Dermatan sulfate degradation [PATH:hsa01100]\n hsa_M00077 Chondroitin sulfate degradation [PATH:hsa01100]\n hsa_M00078 Heparan sulfate degradation [PATH:hsa01100]\n hsa_M00079 Keratan sulfate degradation [PATH:hsa01100]\n hsa_M00082 Fatty acid biosynthesis, initiation [PATH:hsa01100]\n hsa_M00083 Fatty acid biosynthesis, elongation [PATH:hsa01100]\n hsa_M00085 Fatty acid elongation in mitochondria [PATH:hsa01100]\n hsa_M00086 beta-Oxidation, acyl-CoA synthesis [PATH:hsa01100]\n hsa_M00087 beta-Oxidation [PATH:hsa01100]\n hsa_M00089 Triacylglycerol biosynthesis [PATH:hsa01100]\n hsa_M00090 Phosphatidylcholine (PC) biosynthesis, choline => PC [PATH:hsa01100]\n hsa_M00091 Phosphatidylcholine (PC) biosynthesis, PE => PC [PATH:hsa01100]\n hsa_M00092 Phosphatidylethanolamine (PE) biosynthesis, ethanolamine => PE [PATH:hsa01100]\n hsa_M00094 Ceramide biosynthesis [PATH:hsa01100]\n hsa_M00095 C5 isoprenoid biosynthesis, mevalonate pathway [PATH:hsa01100]\n hsa_M00098 Acylglycerol degradation [PATH:hsa01100]\n hsa_M00099 Sphingosine biosynthesis [PATH:hsa01100]\n hsa_M00100 Sphingosine degradation [PATH:hsa01100]\n hsa_M00103 Cholecalciferol biosynthesis [PATH:hsa01100]\n hsa_M00106 Conjugated bile acid biosynthesis, cholate => taurocholate/glycocholate [PATH:hsa01100]\n hsa_M00107 Steroid hormone biosynthesis, cholesterol => pregnenolone => progesterone [PATH:hsa01100]\n hsa_M00108 C21-Steroid hormone biosynthesis, progesterone => corticosterone/aldosterone [PATH:hsa01100]\n hsa_M00109 C21-Steroid hormone biosynthesis, progesterone => cortisol/cortisone [PATH:hsa01100]\n hsa_M00110 C19/C18-Steroid hormone biosynthesis, pregnenolone => androstenedione => estrone [PATH:hsa01100]\n hsa_M00118 Glutathione biosynthesis, glutamate => glutathione [PATH:hsa01100]\n hsa_M00120 Coenzyme A biosynthesis, pantothenate => CoA [PATH:hsa01100]\n hsa_M00128 Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate + polyprenyl-PP => ubiquinone [PATH:hsa01100]\n hsa_M00130 Inositol phosphate metabolism, PI=> PIP2 => Ins(1,4,5)P3 => Ins(1,3,4,5)P4 [PATH:hsa01100]\n hsa_M00131 Inositol phosphate metabolism, Ins(1,3,4,5)P4 => Ins(1,3,4)P3 => myo-inositol [PATH:hsa01100]\n hsa_M00132 Inositol phosphate metabolism, Ins(1,3,4)P3 => phytate [PATH:hsa01100]\n hsa_M00134 Polyamine biosynthesis, arginine => ornithine => putrescine [PATH:hsa01100]\n hsa_M00135 GABA biosynthesis, eukaryotes, putrescine => GABA [PATH:hsa01100]\n hsa_M00141 C1-unit interconversion, eukaryotes [PATH:hsa01100]\n hsa_M00142 NADH:ubiquinone oxidoreductase, mitochondria [PATH:hsa01100]\n hsa_M00143 NADH dehydrogenase (ubiquinone) Fe-S protein/flavoprotein complex, mitochondria [PATH:hsa01100]\n hsa_M00146 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex [PATH:hsa01100]\n hsa_M00147 NADH dehydrogenase (ubiquinone) 1 beta subcomplex [PATH:hsa01100]\n hsa_M00148 Succinate dehydrogenase (ubiquinone) [PATH:hsa01100]\n hsa_M00151 Cytochrome bc1 complex respiratory unit [PATH:hsa01100]\n hsa_M00152 Cytochrome bc1 complex [PATH:hsa01100]\n hsa_M00154 Cytochrome c oxidase [PATH:hsa01100]\n hsa_M00158 F-type ATPase, eukaryotes [PATH:hsa01100]\n hsa_M00160 V-type ATPase, eukaryotes [PATH:hsa01100]\n hsa_M00307 Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa01100]\n hsa_M00338 Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:hsa01100]\n hsa_M00367 C10-C20 isoprenoid biosynthesis, non-plant eukaryotes [PATH:hsa01100]\n hsa_M00415 Fatty acid elongation in endoplasmic reticulum [PATH:hsa01100]\n hsa_M00549 Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH:hsa01100]\n hsa_M00554 Nucleotide sugar biosynthesis, galactose => UDP-galactose [PATH:hsa01100]\n hsa_M00555 Betaine biosynthesis, choline => betaine [PATH:hsa01100]\n hsa_M00621 Glycine cleavage system [PATH:hsa01100]\n hsa_M00632 Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1P [PATH:hsa01100]\n hsa_M00741 Propanoyl-CoA metabolism, propanoyl-CoA => succinyl-CoA [PATH:hsa01100]\n hsa_M00842 Tetrahydrobiopterin biosynthesis, GTP => BH4 [PATH:hsa01100]\n hsa_M00844 Arginine biosynthesis, ornithine => arginine [PATH:hsa01100]\n hsa_M00854 Glycogen biosynthesis, glucose-1P => glycogen/starch [PATH:hsa01100]\n hsa_M00855 Glycogen degradation, glycogen => glucose-6P [PATH:hsa01100]\n hsa_M00861 beta-Oxidation, peroxisome, VLCFA [PATH:hsa01100]\n hsa_M00862 beta-Oxidation, peroxisome, tri/dihydroxycholestanoyl-CoA => choloyl/chenodeoxycholoyl-CoA [PATH:hsa01100]\n hsa_M00868 Heme biosynthesis, animals and fungi, glycine => heme [PATH:hsa01100]\n hsa_M00873 Fatty acid biosynthesis in mitochondria, animals [PATH:hsa01100]\n hsa_M00880 Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor [PATH:hsa01100]\n hsa_M00882 Lipoic acid biosynthesis, eukaryotes, octanoyl-ACP => dihydrolipoyl-H [PATH:hsa01100]\n hsa_M00883 Lipoic acid biosynthesis, animals and bacteria, octanoyl-ACP => dihydrolipoyl-H => dihydrolipoyl-E2 [PATH:hsa01100]\n hsa_M00892 UDP-N-acetyl-D-glucosamine biosynthesis, eukaryotes, glucose => UDP-GlcNAc [PATH:hsa01100]\n hsa_M00912 NAD biosynthesis, tryptophan => quinolinate => NAD [PATH:hsa01100]\n hsa_M00938 Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP [PATH:hsa01100]\n hsa_M00958 Adenine ribonucleotide degradation, AMP => Urate [PATH:hsa01100]\n hsa_M00959 Guanine ribonucleotide degradation, GMP => Urate [PATH:hsa01100]\n hsa_M00970 Proline degradation, proline => glutamate [PATH:hsa01100]\n hsa_M00972 Proline metabolism [PATH:hsa01100]\n hsa_M00974 Betaine metabolism, animals, betaine => glycine [PATH:hsa01100]\n hsa_M00976 C19-Steroid hormone biosynthesis, pregnenolone => testosterone => dihydrotestosterone [PATH:hsa01100]\n hsa_M00977 C19-Steroid hormone biosynthesis (androgen backdoor pathway), pregnenolone => androsterone => dihydrotestosterone [PATH:hsa01100]\n hsa_M00983 GPI-anchor remodeling [PATH:hsa01100]\nDRUG D01392 Mizoribine (JP18/INN)\nORGANISM Homo sapiens (human) [GN:hsa]\nREL_PATHWAY hsa00010 Glycolysis / Gluconeogenesis\n hsa00020 Citrate cycle (TCA cycle)\n hsa00030 Pentose phosphate pathway\n hsa00040 Pentose and glucuronate interconversions\n hsa00051 Fructose and mannose metabolism\n hsa00052 Galactose metabolism\n hsa00053 Ascorbate and aldarate metabolism\n hsa00061 Fatty acid biosynthesis\n hsa00062 Fatty acid elongation\n hsa00071 Fatty acid degradation\n hsa00100 Steroid biosynthesis\n hsa00120 Primary bile acid biosynthesis\n hsa00130 Ubiquinone and other terpenoid-quinone biosynthesis\n hsa00140 Steroid hormone biosynthesis\n hsa00190 Oxidative phosphorylation\n hsa00220 Arginine biosynthesis\n hsa00230 Purine metabolism\n hsa00232 Caffeine metabolism\n hsa00240 Pyrimidine metabolism\n hsa00250 Alanine, aspartate and glutamate metabolism\n hsa00260 Glycine, serine and threonine metabolism\n hsa00270 Cysteine and methionine metabolism\n hsa00280 Valine, leucine and isoleucine degradation\n hsa00290 Valine, leucine and isoleucine biosynthesis\n hsa00310 Lysine degradation\n hsa00330 Arginine and proline metabolism\n hsa00340 Histidine metabolism\n hsa00350 Tyrosine metabolism\n hsa00360 Phenylalanine metabolism\n hsa00380 Tryptophan metabolism\n hsa00400 Phenylalanine, tyrosine and tryptophan biosynthesis\n hsa00410 beta-Alanine metabolism\n hsa00430 Taurine and hypotaurine metabolism\n hsa00440 Phosphonate and phosphinate metabolism\n hsa00450 Selenocompound metabolism\n hsa00470 D-Amino acid metabolism\n hsa00480 Glutathione metabolism\n hsa00500 Starch and sucrose metabolism\n hsa00510 N-Glycan biosynthesis\n hsa00511 Other glycan degradation\n hsa00512 Mucin type O-glycan biosynthesis\n hsa00513 Various types of N-glycan biosynthesis\n hsa00514 Other types of O-glycan biosynthesis\n hsa00515 Mannose type O-glycan biosynthesis\n hsa00520 Amino sugar and nucleotide sugar metabolism\n hsa00524 Neomycin, kanamycin and gentamicin biosynthesis\n hsa00531 Glycosaminoglycan degradation\n hsa00532 Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate\n hsa00533 Glycosaminoglycan biosynthesis - keratan sulfate\n hsa00534 Glycosaminoglycan biosynthesis - heparan sulfate / heparin\n hsa00541 Biosynthesis of various nucleotide sugars\n hsa00561 Glycerolipid metabolism\n hsa00562 Inositol phosphate metabolism\n hsa00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis\n hsa00564 Glycerophospholipid metabolism\n hsa00565 Ether lipid metabolism\n hsa00590 Arachidonic acid metabolism\n hsa00591 Linoleic acid metabolism\n hsa00592 alpha-Linolenic acid metabolism\n hsa00600 Sphingolipid metabolism\n hsa00601 Glycosphingolipid biosynthesis - lacto and neolacto series\n hsa00603 Glycosphingolipid biosynthesis - globo and isoglobo series\n hsa00604 Glycosphingolipid biosynthesis - ganglio series\n hsa00620 Pyruvate metabolism\n hsa00630 Glyoxylate and dicarboxylate metabolism\n hsa00640 Propanoate metabolism\n hsa00650 Butanoate metabolism\n hsa00670 One carbon pool by folate\n hsa00730 Thiamine metabolism\n hsa00740 Riboflavin metabolism\n hsa00750 Vitamin B6 metabolism\n hsa00760 Nicotinate and nicotinamide metabolism\n hsa00770 Pantothenate and CoA biosynthesis\n hsa00780 Biotin metabolism\n hsa00785 Lipoic acid metabolism\n hsa00790 Folate biosynthesis\n hsa00830 Retinol metabolism\n hsa00860 Porphyrin metabolism\n hsa00900 Terpenoid backbone biosynthesis\n hsa00910 Nitrogen metabolism\n hsa00920 Sulfur metabolism\n hsa00980 Metabolism of xenobiotics by cytochrome P450\n hsa00982 Drug metabolism - cytochrome P450\n hsa00983 Drug metabolism - other enzymes\n hsa01040 Biosynthesis of unsaturated fatty acids\nKO_PATHWAY ko01100\n///\n\nENTRY hsa01200 Overview Pathway\nNAME Carbon metabolism - Homo sapiens (human)\nDESCRIPTION Carbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excluding a cofactor (CoA, CoM, THF, or THMPT) that is replaced by an asterisk. The map contains carbon utilization pathways of glycolysis (map00010), pentose phosphate pathway (map00030), and citrate cycle (map00020), and six known carbon fixation pathways (map00710 and map00720) as well as some pathways of methane metabolism (map00680). The six carbon fixation pathways are: (1) reductive pentose phosphate cycle (Calvin cycle) in plants and cyanobacteria that perform oxygenic photosynthesis, (2) reductive citrate cycle in photosynthetic green sulfur bacteria and some chemolithoautotrophs, (3) 3-hydroxypropionate bi-cycle in photosynthetic green nonsulfur bacteria, two variants of 4-hydroxybutyrate pathways in Crenarchaeota called (4) hydroxypropionate-hydroxybutyrate cycle and (5) dicarboxylate-hydroxybutyrate cycle, and (6) reductive acetyl-CoA pathway in methanogenic bacteria.\nPATHWAY_MAP hsa01200 Carbon metabolism\nMODULE hsa_M00001 Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:hsa01200]\n hsa_M00002 Glycolysis, core module involving three-carbon compounds [PATH:hsa01200]\n hsa_M00004 Pentose phosphate pathway (Pentose phosphate cycle) [PATH:hsa01200]\n hsa_M00005 PRPP biosynthesis, ribose 5P => PRPP [PATH:hsa01200]\n hsa_M00006 Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:hsa01200]\n hsa_M00007 Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:hsa01200]\n hsa_M00009 Citrate cycle (TCA cycle, Krebs cycle) [PATH:hsa01200]\n hsa_M00010 Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:hsa01200]\n hsa_M00011 Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:hsa01200]\n hsa_M00020 Serine biosynthesis, glycerate-3P => serine [PATH:hsa01200]\n hsa_M00307 Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa01200]\n hsa_M00621 Glycine cleavage system [PATH:hsa01200]\n hsa_M00741 Propanoyl-CoA metabolism, propanoyl-CoA => succinyl-CoA [PATH:hsa01200]\nORGANISM Homo sapiens (human) [GN:hsa]\nKO_PATHWAY ko01200\n///\n\nENTRY hsa01210 Overview Pathway\nNAME 2-Oxocarboxylic acid metabolism - Homo sapiens (human)\nDESCRIPTION 2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate) and 2-oxoglutarate. This diagram illustrates the architecture of chain extension and modification reaction modules for 2-oxocarboxylic acids. The chain extension module RM001 is a tricarboxylic pathway where acetyl-CoA derived carbon is used to extend the chain length by one. The chain modification modules RM002 (including RM032) and RM033, together with a reductive amination step (RC00006 or RC00036), generate basic and branched-chain amino acids, respectively. The modification module RM030 is used in the biosynthesis of glucosinolates, a class of plant secondary metabolites, for conversion to oxime followed by addition of thio-glucose moiety. Furthermore, the chain extension from 2-oxoadipate to 2-oxosuberate is followed by coenzyme B biosynthesis in methonogenic archaea.\nPATHWAY_MAP hsa01210 2-Oxocarboxylic acid metabolism\nMODULE hsa_M00010 Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:hsa01210]\n hsa_M00011 Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:hsa01210]\n hsa_M00032 Lysine degradation, lysine => saccharopine => acetoacetyl-CoA [PATH:hsa01210]\n hsa_M00307 Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa01210]\nDRUG D10901 Enasidenib (USAN/INN)\n D11044 Enasidenib mesylate (USAN)\n D11090 Ivosidenib (JAN/USAN/INN)\n D12483 Olutasidenib (USAN/INN)\n D12708 Crelosidenib (USAN)\n D12717 Crelosidenib gentisate (USAN)\nORGANISM Homo sapiens (human) [GN:hsa]\nREL_PATHWAY hsa00020 Citrate cycle (TCA cycle)\n hsa00220 Arginine biosynthesis\n hsa00250 Alanine, aspartate and glutamate metabolism\n hsa00260 Glycine, serine and threonine metabolism\n hsa00270 Cysteine and methionine metabolism\n hsa00290 Valine, leucine and isoleucine biosynthesis\n hsa00310 Lysine degradation\n hsa00620 Pyruvate metabolism\n hsa00640 Propanoate metabolism\nKO_PATHWAY ko01210\n///\n\nENTRY hsa01212 Overview Pathway\nNAME Fatty acid metabolism - Homo sapiens (human)\nPATHWAY_MAP hsa01212 Fatty acid metabolism\nMODULE hsa_M00082 Fatty acid biosynthesis, initiation [PATH:hsa01212]\n hsa_M00083 Fatty acid biosynthesis, elongation [PATH:hsa01212]\n hsa_M00085 Fatty acid elongation in mitochondria [PATH:hsa01212]\n hsa_M00086 beta-Oxidation, acyl-CoA synthesis [PATH:hsa01212]\n hsa_M00087 beta-Oxidation [PATH:hsa01212]\n hsa_M00415 Fatty acid elongation in endoplasmic reticulum [PATH:hsa01212]\n hsa_M00861 beta-Oxidation, peroxisome, VLCFA [PATH:hsa01212]\n hsa_M00873 Fatty acid biosynthesis in mitochondria, animals [PATH:hsa01212]\nDRUG D05292 Oxfenicine (USAN/INN)\n D11186 Olumacostat glasaretil (USAN/INN)\n D11640 Firsocostat (USAN/INN)\n D11902 Clesacostat (USAN)\n D11903 Clesacostat tromethamine (USAN)\n D12391 Denifanstat (USAN/INN)\nORGANISM Homo sapiens (human) [GN:hsa]\nREL_PATHWAY hsa00020 Citrate cycle (TCA cycle)\nKO_PATHWAY ko01212\n///\n\nENTRY hsa01230 Overview Pathway\nNAME Biosynthesis of amino acids - Homo sapiens (human)\nDESCRIPTION This map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module for conversion of three-carbon compounds from glyceraldehyde-3P to pyruvate [MD:M00002], together with the pathways around serine and glycine. This KEGG module is the most conserved one in the KEGG MODULE database and is found in almost all the completely sequenced genomes. The extensions are the pathways containing the reaction modules RM001, RM033, RM032, and RM002 for biosynthesis of branched-chain amino acids (left) and basic amino acids (bottom), and the pathways for biosynthesis of histidine and aromatic amino acids (top right). It is interesting to note that the so-called essential amino acids that cannot be synthesized in human and other organisms generally appear in these extensions. Furthermore, the bottom extension of basic amino acids appears to be most divergent containing multiple pathways for lysine biosynthesis and multiple gene sets for arginine biosynthesis.\nPATHWAY_MAP hsa01230 Biosynthesis of amino acids\nMODULE hsa_M00002 Glycolysis, core module involving three-carbon compounds [PATH:hsa01230]\n hsa_M00005 PRPP biosynthesis, ribose 5P => PRPP [PATH:hsa01230]\n hsa_M00007 Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:hsa01230]\n hsa_M00010 Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:hsa01230]\n hsa_M00015 Proline biosynthesis, glutamate => proline [PATH:hsa01230]\n hsa_M00020 Serine biosynthesis, glycerate-3P => serine [PATH:hsa01230]\n hsa_M00029 Urea cycle [PATH:hsa01230]\n hsa_M00338 Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:hsa01230]\n hsa_M00844 Arginine biosynthesis, ornithine => arginine [PATH:hsa01230]\nDRUG D10901 Enasidenib (USAN/INN)\n D11044 Enasidenib mesylate (USAN)\n D11695 Pegzilarginase (USAN/INN)\nORGANISM Homo sapiens (human) [GN:hsa]\nKO_PATHWAY ko01230\n///\n\nENTRY hsa01232 Overview Pathway\nNAME Nucleotide metabolism - Homo sapiens (human)\nPATHWAY_MAP hsa01232 Nucleotide metabolism\nMODULE hsa_M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:hsa01232]\n hsa_M00050 Guanine ribonucleotide biosynthesis, IMP => GDP,GTP [PATH:hsa01232]\n hsa_M00052 Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:hsa01232]\n hsa_M00053 Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP [PATH:hsa01232]\n hsa_M00938 Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP [PATH:hsa01232]\n hsa_M00958 Adenine ribonucleotide degradation, AMP => Urate [PATH:hsa01232]\n hsa_M00959 Guanine ribonucleotide degradation, GMP => Urate [PATH:hsa01232]\nDRUG D11447 Arfolitixorin (USAN/INN)\n D12387 Fosgemcitabine palabenamide (USAN/INN)\n D12388 Fosifloxuridine nafalbenamide\n D12465 Doxecitine (USAN/INN)\n D12466 Doxribtimine (USAN/INN)\n D12528 Arfolitixorin sulfate (JAN)\nORGANISM Homo sapiens (human) [GN:hsa]\nKO_PATHWAY ko01232\n///\n\nENTRY hsa01250 Overview Pathway\nNAME Biosynthesis of nucleotide sugars - Homo sapiens (human)\nPATHWAY_MAP hsa01250 Biosynthesis of nucleotide sugars\nMODULE hsa_M00549 Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH:hsa01250]\n hsa_M00554 Nucleotide sugar biosynthesis, galactose => UDP-galactose [PATH:hsa01250]\n hsa_M00892 UDP-N-acetyl-D-glucosamine biosynthesis, eukaryotes, glucose => UDP-GlcNAc [PATH:hsa01250]\n hsa_M00955 CMP-Neu5Ac/Neu5Gc biosynthesis, animals, UDP-GlcNAc => CMP-Neu5Ac => CMP-Neu5Gc [PATH:hsa01250]\nORGANISM Homo sapiens (human) [GN:hsa]\nKO_PATHWAY ko01250\n///\n\nENTRY hsa01240 Overview Pathway\nNAME Biosynthesis of cofactors - Homo sapiens (human)\nPATHWAY_MAP hsa01240 Biosynthesis of cofactors\nMODULE hsa_M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:hsa01240]\n hsa_M00051 De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMP [PATH:hsa01240]\n hsa_M00052 Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:hsa01240]\n hsa_M00118 Glutathione biosynthesis, glutamate => glutathione [PATH:hsa01240]\n hsa_M00120 Coenzyme A biosynthesis, pantothenate => CoA [PATH:hsa01240]\n hsa_M00128 Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate + polyprenyl-PP => ubiquinone [PATH:hsa01240]\n hsa_M00141 C1-unit interconversion, eukaryotes [PATH:hsa01240]\n hsa_M00842 Tetrahydrobiopterin biosynthesis, GTP => BH4 [PATH:hsa01240]\n hsa_M00868 Heme biosynthesis, animals and fungi, glycine => heme [PATH:hsa01240]\n hsa_M00880 Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor [PATH:hsa01240]\n hsa_M00882 Lipoic acid biosynthesis, eukaryotes, octanoyl-ACP => dihydrolipoyl-H [PATH:hsa01240]\n hsa_M00883 Lipoic acid biosynthesis, animals and bacteria, octanoyl-ACP => dihydrolipoyl-H => dihydrolipoyl-E2 [PATH:hsa01240]\n hsa_M00912 NAD biosynthesis, tryptophan => quinolinate => NAD [PATH:hsa01240]\nDRUG D12991 Efzimfotase alfa (USAN/INN)\nORGANISM Homo sapiens (human) [GN:hsa]\nKO_PATHWAY ko01240\n///\n\nENTRY hsa01320 Overview Pathway\nNAME Sulfur cycle - Homo sapiens (human)\nDESCRIPTION Sulfur is one of the six most common chemical elements CHNOPS that constitute living organisms. This map shows a biogeochemical cycle of sulfur compounds and how different microorganisms are responsible for chemical transformations under different environments including atmospheric, hydrospheric and lithospheric environments. Details of chemical reactions and responsible enzymes are shown in map00920 for Sulfur metabolism. Here chemical transformations are represented by KEGG modules, including sulfur reduction [MD:M00986] [KO:K16952] from elemental sulfur to hydrogen sulfide by sulfur-reducing bacteria and archaea, sulfide oxidation [MD:M00985] from hydrogen sulfide to elemental sulfur by sulfur-oxidizing phototrophs, sulfur oxidataion [MD:M00595 M00984] from thiosulfate to sulfate by sulfur-oxidizing chemotrophs, dissimilatory sulfate reduction [MD:M00596] by sulfate-reducing bacteria and archaea, and assimilatory sulfate reduction [MD:M00176 M00987] by both prokaryotes and eukaryotes excluding animals.\nPATHWAY_MAP hsa01320 Sulfur cycle\nORGANISM Homo sapiens (human) [GN:hsa]\nKO_PATHWAY ko01320\n///\n\nENTRY hsa00010 Pathway\nNAME Glycolysis / Gluconeogenesis - Homo sapiens (human)\nDESCRIPTION Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, another important precursor metabolite, is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes, the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002], which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003].\nCLASS Metabolism; Carbohydrate metabolism\nPATHWAY_MAP hsa00010 Glycolysis / Gluconeogenesis\nMODULE hsa_M00001 Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:hsa00010]\n hsa_M00002 Glycolysis, core module involving three-carbon compounds [PATH:hsa00010]\n hsa_M00003 Gluconeogenesis, oxaloacetate => fructose-6P [PATH:hsa00010]\n hsa_M00307 Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa00010]\nNETWORK nt06017 Glycogen metabolism\n ELEMENT N00731 Glycolysis\nDRUG D00123 Cyanamide (JP18)\n D00131 Disulfiram (JP18/USP/INN)\n D07257 Lonidamine (INN)\n D08970 Piragliatin (USAN)\n D11342 Dorzagliatin (USAN)\n D11408 Mitapivat sulfate (USAN)\n D12320 Cadisegliatin (USAN)\n D12362 Etavopivat (USAN/INN)\n D13032 Tebapivat (USAN/INN)\nDBLINKS GO: 0006096 0006094\nORGANISM Homo sapiens (human) [GN:hsa]\nGENE 10327 AKR1A1; aldo-keto reductase family 1 member A1 [KO:K00002] [EC:1.1.1.2]\n 124 ADH1A; alcohol dehydrogenase 1A (class I), alpha polypeptide [KO:K13951] [EC:1.1.1.1]\n 125 ADH1B; alcohol dehydrogenase 1B (class I), beta polypeptide [KO:K13951] [EC:1.1.1.1]\n 126 ADH1C; alcohol dehydrogenase 1C (class I), gamma polypeptide [KO:K13951] [EC:1.1.1.1]\n 127 ADH4; alcohol dehydrogenase 4 (class II), pi polypeptide [KO:K13980] [EC:1.1.1.1]\n 128 ADH5; alcohol dehydrogenase 5 (class III), chi polypeptide [KO:K00121] [EC:1.1.1.284 1.1.1.1]\n 130 ADH6; alcohol dehydrogenase 6 (class V) [KO:K13952] [EC:1.1.1.1]\n 130589 GALM; galactose mutarotase [KO:K01785] [EC:5.1.3.3]\n 131 ADH7; alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide [KO:K13951] [EC:1.1.1.1]\n 160287 LDHAL6A; lactate dehydrogenase A like 6A [KO:K00016] [EC:1.1.1.27]\n 1737 DLAT; dihydrolipoamide S-acetyltransferase [KO:K00627] [EC:2.3.1.12]\n 1738 DLD; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]\n 2023 ENO1; enolase 1 [KO:K01689] [EC:4.2.1.11]\n 2026 ENO2; enolase 2 [KO:K01689] [EC:4.2.1.11]\n 2027 ENO3; enolase 3 [KO:K01689] [EC:4.2.1.11]\n 217 ALDH2; aldehyde dehydrogenase 2 family member [KO:K00128] [EC:1.2.1.3]\n 218 ALDH3A1; aldehyde dehydrogenase 3 family member A1 [KO:K00129] [EC:1.2.1.5]\n 219 ALDH1B1; aldehyde dehydrogenase 1 family member B1 [KO:K00128] [EC:1.2.1.3]\n 2203 FBP1; fructose-bisphosphatase 1 [KO:K03841] [EC:3.1.3.11]\n 221 ALDH3B1; aldehyde dehydrogenase 3 family member B1 [KO:K00129] [EC:1.2.1.5]\n 222 ALDH3B2; aldehyde dehydrogenase 3 family member B2 [KO:K00129] [EC:1.2.1.5]\n 223 ALDH9A1; aldehyde dehydrogenase 9 family member A1 [KO:K00149] [EC:1.2.1.47 1.2.1.3]\n 224 ALDH3A2; aldehyde dehydrogenase 3 family member A2 [KO:K00128] [EC:1.2.1.3]\n 226 ALDOA; aldolase, fructose-bisphosphate A [KO:K01623] [EC:4.1.2.13]\n 229 ALDOB; aldolase, fructose-bisphosphate B [KO:K01623] [EC:4.1.2.13]\n 230 ALDOC; aldolase, fructose-bisphosphate C [KO:K01623] [EC:4.1.2.13]\n 2538 G6PC1; glucose-6-phosphatase catalytic subunit 1 [KO:K01084] [EC:3.1.3.9]\n 2597 GAPDH; glyceraldehyde-3-phosphate dehydrogenase [KO:K00134] [EC:1.2.1.12]\n 26330 GAPDHS; glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [KO:K10705] [EC:1.2.1.12]\n 2645 GCK; glucokinase [KO:K12407] [EC:2.7.1.2]\n 2821 GPI; glucose-6-phosphate isomerase [KO:K01810] [EC:5.3.1.9]\n 3098 HK1; hexokinase 1 [KO:K00844] [EC:2.7.1.1]\n 3099 HK2; hexokinase 2 [KO:K00844] [EC:2.7.1.1]\n 3101 HK3; hexokinase 3 [KO:K00844] [EC:2.7.1.1]\n 387712 ENO4; enolase 4 [KO:K27394]\n 3939 LDHA; lactate dehydrogenase A [KO:K00016] [EC:1.1.1.27]\n 3945 LDHB; lactate dehydrogenase B [KO:K00016] [EC:1.1.1.27]\n 3948 LDHC; lactate dehydrogenase C [KO:K00016] [EC:1.1.1.27]\n 441531 PGAM4; phosphoglycerate mutase family member 4 [KO:K01834] [EC:5.4.2.11]\n 501 ALDH7A1; aldehyde dehydrogenase 7 family member A1 [KO:K14085] [EC:1.2.1.31 1.2.1.8 1.2.1.3]\n 5105 PCK1; phosphoenolpyruvate carboxykinase 1 [KO:K01596] [EC:4.1.1.32]\n 5106 PCK2; phosphoenolpyruvate carboxykinase 2, mitochondrial [KO:K01596] [EC:4.1.1.32]\n 5160 PDHA1; pyruvate dehydrogenase E1 subunit alpha 1 [KO:K00161] [EC:1.2.4.1]\n 5161 PDHA2; pyruvate dehydrogenase E1 subunit alpha 2 [KO:K00161] [EC:1.2.4.1]\n 5162 PDHB; pyruvate dehydrogenase E1 subunit beta [KO:K00162] [EC:1.2.4.1]\n 5211 PFKL; phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]\n 5213 PFKM; phosphofructokinase, muscle [KO:K00850] [EC:2.7.1.11]\n 5214 PFKP; phosphofructokinase, platelet [KO:K00850] [EC:2.7.1.11]\n 5223 PGAM1; phosphoglycerate mutase 1 [KO:K01834] [EC:5.4.2.11]\n 5224 PGAM2; phosphoglycerate mutase 2 [KO:K01834] [EC:5.4.2.11]\n 5230 PGK1; phosphoglycerate kinase 1 [KO:K00927] [EC:2.7.2.3]\n 5232 PGK2; phosphoglycerate kinase 2 [KO:K00927] [EC:2.7.2.3]\n 5236 PGM1; phosphoglucomutase 1 [KO:K01835] [EC:5.4.2.2]\n 5313 PKLR; pyruvate kinase L/R [KO:K12406] [EC:2.7.1.40]\n 5315 PKM; pyruvate kinase M1/2 [KO:K00873] [EC:2.7.1.40]\n 55276 PGM2; phosphoglucomutase 2 [KO:K15779] [EC:5.4.2.2 5.4.2.7]\n 55902 ACSS2; acyl-CoA synthetase short chain family member 2 [KO:K01895] [EC:6.2.1.1]\n 57818 G6PC2; glucose-6-phosphatase catalytic subunit 2 [KO:K01084] [EC:3.1.3.9]\n 669 BPGM; bisphosphoglycerate mutase [KO:K01837] [EC:5.4.2.4 5.4.2.11]\n 7167 TPI1; triosephosphate isomerase 1 [KO:K01803] [EC:5.3.1.1]\n 80201 HKDC1; hexokinase domain containing 1 [KO:K00844] [EC:2.7.1.1]\n 83440 ADPGK; ADP dependent glucokinase [KO:K08074] [EC:2.7.1.147]\n 84532 ACSS1; acyl-CoA synthetase short chain family member 1 [KO:K01895] [EC:6.2.1.1]\n 8789 FBP2; fructose-bisphosphatase 2 [KO:K03841] [EC:3.1.3.11]\n 92483 LDHAL6B; lactate dehydrogenase A like 6B [KO:K00016] [EC:1.1.1.27]\n 92579 G6PC3; glucose-6-phosphatase catalytic subunit 3 [KO:K01084] [EC:3.1.3.9]\n 9562 MINPP1; multiple inositol-polyphosphate phosphatase 1 [KO:K03103] [EC:3.1.3.62 3.1.3.80]\nCOMPOUND C00022 Pyruvate\n C00024 Acetyl-CoA\n C00031 D-Glucose\n C00033 Acetate\n C00036 Oxaloacetate\n C00068 Thiamin diphosphate\n C00074 Phosphoenolpyruvate\n C00084 Acetaldehyde\n C00085 D-Fructose 6-phosphate\n C00103 D-Glucose 1-phosphate\n C00111 Glycerone phosphate\n C00118 D-Glyceraldehyde 3-phosphate\n C00186 (S)-Lactate\n C00197 3-Phospho-D-glycerate\n C00221 beta-D-Glucose\n C00236 3-Phospho-D-glyceroyl phosphate\n C00267 alpha-D-Glucose\n C00354 D-Fructose 1,6-bisphosphate\n C00469 Ethanol\n C00631 2-Phospho-D-glycerate\n C00668 alpha-D-Glucose 6-phosphate\n C01159 2,3-Bisphospho-D-glycerate\n C01172 beta-D-Glucose 6-phosphate\n C01451 Salicin\n C05125 2-(alpha-Hydroxyethyl)thiamine diphosphate\n C06186 Arbutin\n C06187 Arbutin 6-phosphate\n C06188 Salicin 6-phosphate\n C15972 Enzyme N6-(lipoyl)lysine\n C15973 Enzyme N6-(dihydrolipoyl)lysine\n C16255 [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine\nREFERENCE \n AUTHORS Nishizuka Y (ed).\n TITLE [Metabolic Maps] (In Japanese)\n JOURNAL Tokyo Kagaku Dojin (1980)\nREFERENCE \n AUTHORS Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).\n TITLE [Cellular Functions and Metabolic Maps] (In Japanese)\n JOURNAL Tokyo Kagaku Dojin (1997)\nREFERENCE \n AUTHORS Michal G.\n TITLE Biochemical Pathways\n JOURNAL Wiley (1999)\nREL_PATHWAY hsa00020 Citrate cycle (TCA cycle)\n hsa00030 Pentose phosphate pathway\n hsa00500 Starch and sucrose metabolism\n hsa00620 Pyruvate metabolism\n hsa00640 Propanoate metabolism\nKO_PATHWAY ko00010\n///")
8. └─ffrec$setBody(value)
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